Mercurial > repos > chemteam > gmx_fep

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alchemical_run/gmx_fep.sh	Mon Nov 11 13:20:39 2019 -0500
@@ -0,0 +1,114 @@
+#!/bin/bash
+
+# _________ read inputs from the galaxy wrapper and define some variables ____________
+
+lam=$1
+iter=$((lam+1))
+
+mkdir MDP
+mkdir data
+mkdir traj
+
+FREE_ENERGY=`pwd`
+MDP=$FREE_ENERGY/MDP
+
+
+for i in `seq 0 $lam`
+ do
+   cp em_steep.mdp em_steep_$i.mdp
+   sed -i "s/%L%/$i/" em_steep_$i.mdp
+   cp nvt.mdp nvt_$i.mdp
+   sed -i "s/%L%/$i/" nvt_$i.mdp
+   cp npt.mdp npt_$i.mdp
+   sed -i "s/%L%/$i/" npt_$i.mdp
+   cp md.mdp md_$i.mdp
+   sed -i "s/%L%/$i/" md_$i.mdp
+ done
+mv *.mdp $MDP
+
+for (( i=0; i<$iter; i++ ))
+do
+    LAMBDA=$i
+
+    # A new directory will be created for each value of lambda
+
+    mkdir Lambda_$LAMBDA
+    cd Lambda_$LAMBDA
+
+# _______ ENERGY MINIMIZATION STEEP _______
+
+    echo "Starting minimization for lambda = $LAMBDA..."
+
+    mkdir EM
+    cd EM
+
+    # Iterative calls to grompp and mdrun to run the simulations
+
+    gmx grompp -f $MDP/em_steep_$LAMBDA.mdp -c $FREE_ENERGY/morph.gro -p $FREE_ENERGY/morph.top -o min$LAMBDA.tpr
+
+    gmx mdrun -deffnm min$LAMBDA
+
+    sleep 10
+
+
+# _______ NVT EQUILIBRATION _______
+
+    echo "Starting constant volume equilibration..."
+
+    cd ../
+    mkdir NVT
+    cd NVT
+
+    gmx grompp -f $MDP/nvt_$LAMBDA.mdp -c ../EM/min$LAMBDA.gro -p $FREE_ENERGY/morph.top -o nvt$LAMBDA.tpr
+
+    gmx mdrun -deffnm nvt$LAMBDA
+
+    echo "Constant volume equilibration complete."
+
+    sleep 10
+
+# _______ NPT EQUILIBRATION _______
+
+    echo "Starting constant pressure equilibration..."
+
+    cd ../
+    mkdir NPT
+    cd NPT
+
+    gmx grompp -f $MDP/npt_$LAMBDA.mdp -c ../NVT/nvt$LAMBDA.gro -p $FREE_ENERGY/morph.top -t ../NVT/nvt$LAMBDA.cpt -o npt$LAMBDA.tpr
+
+    gmx mdrun -deffnm npt$LAMBDA
+
+    echo "Constant pressure equilibration complete."
+
+    sleep 10
+
+# ________ PRODUCTION MD ___________
+
+    echo "Starting production MD simulation..."
+
+    cd ../
+    mkdir Production_MD
+    cd Production_MD
+
+    gmx grompp -f $MDP/md_$LAMBDA.mdp -c ../NPT/npt$LAMBDA.gro -p $FREE_ENERGY/morph.top -t ../NPT/npt$LAMBDA.cpt -o md$LAMBDA.tpr
+
+    gmx mdrun -deffnm md$LAMBDA
+
+    echo "Production MD complete."
+
+    # End
+    echo "Ending. Job completed for lambda = $LAMBDA"
+
+    cd $FREE_ENERGY
+done
+
+cp Lambda_*/Production_MD/*.xvg data/
+tar cf data.tar data/
+
+cp Lambda_*/Production_MD/*.trr traj/
+tar cf traj.tar traj/
+
+exit;
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alchemical_run/gmx_fep.xml	Mon Nov 11 13:20:39 2019 -0500
@@ -0,0 +1,552 @@
+<tool id="gmx_fep" name="Alchemical Run" version="2019.1">
+    <description>Alchemical free energy simulations using gromacs</description>
+    <requirements>
+         <requirement type="package" version="2019.1">gromacs</requirement>
+    </requirements>
+<command detect_errors="exit_code"><![CDATA[
+    ln -s '$em_steep' ./em_steep.mdp &&
+    ln -s '$nvt' ./nvt.mdp &&
+    ln -s '$npt' ./npt.mdp &&
+    ln -s '$md' ./md.mdp &&
+
+    ln -s '$groin' ./morph.gro &&
+    ln -s '$topin' ./morph.top &&
+
+    #if $input_fep == 'perform':
+      bash '$__tool_directory__/gmx_fep.sh' '$path.lambda' &>> '$report'
+    #end if
+    #if $input_fep == 'generate':
+       mkdir -p input_files &&
+       cp '$__tool_directory__/gmx_fep.sh'  input_files/ &&
+       cp ./em_steep.mdp input_files/ &&
+       cp ./nvt.mdp input_files/ &&
+       cp ./npt.mdp input_files/ &&
+       cp ./md.mdp input_files/ &&
+       cp ./morph.gro input_files/ &&
+       cp ./morph.top input_files/ &&
+       tar cf input_files.tar input_files/
+    #end if
+    ]]></command>
+     <configfiles>
+         <configfile name="em_steep">
+integrator               = steep
+nsteps                   = $minstep
+emtol                    = 100
+emstep                   = 0.01
+niter                    = 20
+nbfgscorr                = 10
+nstlog                   = 1
+nstenergy                = 1
+cutoff-scheme            = verlet
+nstlist                  = 10
+ns_type                  = grid
+pbc                      = xyz
+rlist                    = 1.2
+coulombtype              = PME
+rcoulomb                 = 1.2
+vdwtype                  = cutoff
+vdw-modifier             = potential-switch
+rvdw-switch              = 1.0
+rvdw                     = 1.2
+DispCorr                  = EnerPres
+fourierspacing           = 0.12
+pme_order                = 6
+ewald_rtol               = 1e-06
+epsilon_surface          = 0
+tcoupl                   = no
+pcoupl                   = no
+ld-seed                  = -1
+gen-seed                 = $seed
+free_energy              = no
+delta_lambda             = 0
+calc_lambda_neighbors    = 1
+init-lambda-state        = %L%
+
+#if $path.select_path == "global":
+fep-lambdas              = $path.fep
+#end if
+
+#if $path.select_path in ["default1", "default2"]:
+coul-lambdas             = $path.coul
+vdw-lambdas              = $path.vdw
+bonded-lambdas           = $path.bonded
+#end if
+
+sc-alpha                 = 0.5
+sc-coul                  = no
+sc-power                 = 1
+sc-sigma                 = 0.3
+nstdhdl                  = 10
+
+gen_vel                  = no
+constraints              = none
+         </configfile>
+         <configfile name="nvt">
+integrator               = sd
+tinit                    = 0
+dt                       = $dt
+nsteps                   = $nvtstep
+nstcomm                  = 100
+nstxout                  = 500
+nstvout                  = 500
+nstfout                  = 0
+nstlog                   = 500
+nstenergy                = 500
+nstxout-compressed       = 0
+cutoff-scheme            = verlet
+nstlist                  = 20
+ns_type                  = grid
+pbc                      = xyz
+rlist                    = 1.2
+coulombtype              = PME
+rcoulomb                 = 1.2
+vdwtype                  = cutoff
+vdw-modifier             = potential-switch
+rvdw-switch              = 1.0
+rvdw                     = 1.2
+DispCorr                  = EnerPres
+fourierspacing           = 0.12
+pme_order                = 6
+ewald_rtol               = 1e-06
+epsilon_surface          = 0
+tc_grps                  = system
+tau_t                    = 1.0
+ref_t                    = $temperature
+Pcoupl                   = No
+tau_p                    = 0.5
+compressibility          = 4.5e-05
+ref_p                    = $pressure
+ld-seed                  = -1
+gen-seed                 = $seed
+free_energy              = no
+delta_lambda             = 0
+calc_lambda_neighbors    = 1
+init-lambda-state        = %L%
+
+#if $path.select_path == "global":
+fep-lambdas              = $path.fep
+#end if
+
+#if $path.select_path in ["default1", "default2"]:
+coul-lambdas             = $path.coul
+vdw-lambdas              = $path.vdw
+bonded-lambdas           = $path.bonded
+#end if
+
+sc-alpha                 = 0.5
+sc-coul                  = no
+sc-power                 = 1
+sc-sigma                 = 0.3
+nstdhdl                  = 10
+gen_vel                  = yes
+gen_temp                 = 300
+
+#if $constraints.cons == "no":
+constraints              = none
+#end if
+
+#if $constraints.cons == "yes":
+constraints              = $constraints.cons_type
+constraint-algorithm     = lincs
+lincs-order              = $constraints.lincs_order
+lincs-iter               = $constraints.lincs_iter
+lincs-warnangle          = $constraints.lincs_warnangle
+#end if
+         </configfile>
+         <configfile name="npt">
+integrator               = sd
+tinit                    = 0
+dt                       = $dt
+nsteps                   = $nptstep
+nstcomm                  = 100
+nstxout                  = 500
+nstvout                  = 500
+nstfout                  = 0
+nstlog                   = 500
+nstenergy                = 500
+nstxout-compressed       = 0
+cutoff-scheme            = verlet
+nstlist                  = 20
+ns_type                  = grid
+pbc                      = xyz
+rlist                    = 1.2
+coulombtype              = PME
+rcoulomb                 = 1.2
+vdwtype                  = cutoff
+vdw-modifier             = potential-switch
+rvdw-switch              = 1.0
+rvdw                     = 1.2
+DispCorr                  = EnerPres
+fourierspacing           = 0.12
+pme_order                = 6
+ewald_rtol               = 1e-06
+epsilon_surface          = 0
+tc_grps                  = System
+tau_t                    = 1.0
+ref_t                    = $temperature
+Pcoupl                   = Berendsen
+tau_p                    = 0.5
+compressibility          = 4.5e-05
+ref_p                    = $pressure
+ld-seed                  = -1
+gen-seed                 = $seed
+free_energy              = no
+delta_lambda             = 0
+calc_lambda_neighbors    = 1
+init-lambda-state        = %L%
+
+#if $path.select_path == "global":
+fep-lambdas              = $path.fep
+#end if
+
+#if $path.select_path in ["default1", "default2"]:
+coul-lambdas             = $path.coul
+vdw-lambdas              = $path.vdw
+bonded-lambdas           = $path.bonded
+#end if
+
+; Options for the decoupling
+sc-alpha                 = 0.5
+sc-coul                  = no
+sc-power                 = 1
+sc-sigma                 = 0.3
+nstdhdl                  = 10
+gen_vel                  = no
+
+#if $constraints.cons == "no":
+constraints              = none
+#end if
+
+#if $constraints.cons == "yes":
+constraints              = $constraints.cons_type
+constraint-algorithm     = lincs
+lincs-order              = $constraints.lincs_order
+lincs-iter               = $constraints.lincs_iter
+lincs-warnangle          = $constraints.lincs_warnangle
+#end if
+         </configfile>
+         <configfile name="md">
+integrator               = sd
+bd-fric                  = 0
+dt                       = $dt
+nsteps                   = $mdstep
+nstcomm                  = 100
+
+nstxout                  = 10000
+nstvout                  = 0
+nstfout                  = 0
+nstlog                   = 10000
+nstenergy                = 10000
+nstxout-compressed       = 0
+
+tcoupl                   = no
+nsttcouple               = 10
+tc_grps                  = System
+tau_t                    = 1.0
+ref_t                    = $temperature
+
+#if $constraints.cons == "no":
+constraints              = none
+#end if
+
+#if $constraints.cons == "yes":
+constraints              = $constraints.cons_type
+constraint-algorithm     = lincs
+lincs-order              = $constraints.lincs_order
+lincs-iter               = $constraints.lincs_iter
+lincs-warnangle          = $constraints.lincs_warnangle
+#end if
+
+comm-mode                = Linear
+
+cutoff-scheme            = Verlet
+nstlist                  = 10
+ns_type                  = grid
+pbc                      = xyz
+rlist                    = 0.8
+
+coulombtype              = PME
+coulomb-modifier         = none
+rcoulomb                 = 0.8
+fourierspacing           = 0.10
+pme_order                = 4
+ewald_rtol               = 1.0E-5
+
+vdwtype                  = cut-off
+vdw-modifier             = none
+rvdw                     = 0.8
+DispCorr                 = AllEnerPres
+
+pcoupl                   = Parrinello-Rahman
+pcoupltype               = isotropic
+tau_p                    = 2
+compressibility          = 4.5e-5
+ref_p                    = $pressure
+refcoord-scaling         = com
+
+gen-vel                  = no
+continuation             = yes
+
+ld-seed                  = -1
+gen-seed                 = $seed
+
+free-energy              = yes
+delta-lambda             = 0  ; do not use slow growth method
+init-lambda-state        = %L%
+
+#if $path.select_path == "global":
+fep-lambdas              = $path.fep
+#end if
+
+#if $path.select_path in ["default1", "default2"]:
+coul-lambdas             = $path.coul
+vdw-lambdas              = $path.vdw
+bonded-lambdas           = $path.bonded
+#end if
+
+nstdhdl                  = 10
+nstcalcenergy            = 10
+calc-lambda-neighbors    = -1
+
+#if $feoptions.feop == "default":
+sc-alpha                 = 0.5
+sc-coul                  = no
+sc-power                 = 1
+sc-r-power               = 6
+sc-sigma                 = 0.3
+couple-lambda0           = vdw-q
+couple-lambda1           = none
+couple-intramol          = no
+#end if
+
+#if $feoptions.feop == "modify":
+sc-alpha                 = $feoptions.scalpha
+sc-coul                  = $feoptions.sccoul
+sc-power                 = $feoptions.scpower
+sc-r-power               = $feoptions.scrpower
+sc-sigma                 = $feoptions.scsigma
+couple-lambda0           = $feoptions.couplelambda0
+couple-lambda1           = $feoptions.couplelambda1
+couple-intramol          = $feoptions.coupleintramol
+#end if
+
+dhdl-derivatives         = yes
+dhdl-print-energy        = no
+separate-dhdl-file       = yes
+dh_hist_size             = 0
+dh_hist_spacing          = 0.1
+
+         </configfile>
+    </configfiles>
+    <inputs>
+        <param format="gro" name="groin" type="data" label="Structure (GRO) file" help="GRO input file with the merged structure."/>
+        <param format="top" name="topin" type="data" label="Topology (TOP) file" help="TOP input file with the merged structure."/>
+        <param name="minstep"  type="integer" value="10000" label="Minimization steps" help="Number of steps for each free energy window."/>
+        <param name="nvtstep"  type="integer" value="500000" label="NVT equilibration steps" help="Number of MD steps for NVT equilibration for each free energy window."/>
+        <param name="nptstep"  type="integer" value="500000" label="NPT equilibration steps" help="Number of MD steps for NPT equilibration for each free energy window."/>
+        <param name="mdstep"   type="integer" value="1000000" label="MD (production) steps" help="Number of MD steps for production runs of each free energy window."/>
+        <param name="seed"   type="integer" value="19880924" label="Seed" help="Seed to initialize random generator for random velocities."/>
+        <param name="dt" type="float" value="0.001" label="Time step (ps)" help="Time step for integration."/>
+        <conditional name="constraints">
+            <param name="cons" type="select" label="Apply constraints to the ligands?" help="Constraints may be required to keep the ligands with alchemical states in the active site.">
+                <option value="yes">Yes</option>
+                <option value="no">No</option>
+            </param>
+            <when value="no"/>
+            <when value="yes">
+            <param name="cons_type" type="select" label="Constraints type" help="Convert all bonds to constraints, or only those containing hydrogen atoms">
+                <option value="h-bonds" selected="true">H-bonds</option>
+                <option value="all-bonds">All bonds</option>
+            </param>
+            <param name="lincs_order" type="integer" value="4" label="LINCS order" help="Accuracy of LINCS algorithm. For normal MD simulations an order of 4 usually suffices, 6 is needed for large time-steps with virtual sites or BD."/>
+            <param name="lincs_iter" type="integer" value="1" label="LINCS iterations" help="Number of iterations to correct for rotational lengthening in LINCS. For normal runs a single step is sufficient."/>
+            <param name="lincs_warnangle" type="integer" value="30" label="LINCS maximum angle" help="Maximum angle that a bond can rotate before LINCS will complain / [deg]"/>
+            </when>
+        </conditional>
+        <conditional name="path">
+            <param name="select_path" type="select" label="Select the FEP path">
+                <option value="global">Use global lambda scaling</option>
+                <option value="default1">Default option 1 (change a larger ligand to a smaller ligand)</option>
+                <option value="default2">Default option 2 (change a smaller ligand to a larger ligand)</option>
+            </param>
+            <when value="global">
+               <param name="lambda" type="text" value="2" label="Number of free energy windows"/>
+               <param name="fep"  type="text" value="0.00 0.50 1.00" label="FEP Lambdas" help="Global scaling - values must be between 0 and 1."/>
+            </when>
+            <when value="default1">
+               <param name="lambda" type="text" value="40" label="Number of free energy windows"/>
+               <param name="coul"   type="text" value="0.00 0.11 0.22 0.33 0.44 0.56 0.67 0.78 0.89 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.000 1.00" label="Coulomb Lambdas (scaling electrostatics)" help="Values must be between 0 and 1."/>
+               <param name="vdw"    type="text" value="0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.04 0.08 0.11 0.15 0.19 0.23 0.27 0.30 0.34 0.38 0.42 0.46 0.49 0.53 0.57 0.61 0.65 0.68 0.72 0.76 0.80 0.84 0.87 0.91 0.95 0.97 0.98 0.99 0.999 1.00" label="Van der Waals Lambdas (scaling vdw interactions)" help="Values must be between 0 and 1."/>
+               <param name="bonded" type="text" value="0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.04 0.08 0.11 0.15 0.19 0.23 0.27 0.30 0.34 0.38 0.42 0.46 0.49 0.53 0.57 0.61 0.65 0.68 0.72 0.76 0.80 0.84 0.87 0.91 0.95 0.97 0.98 0.99 0.999 1.00" label="Bonded Lambdas (scaling torsion)" help="Values must be between 0 and 1."/>
+            </when>
+            <when value="default2">
+               <param name="lambda" type="text" value="40" label="Number of free energy windows"/>
+               <param name="coul"   type="text" value="0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.000 0.00 0.11 0.22 0.33 0.44 0.56 0.67 0.78 0.89 1.00 " label="Coulomb Lambdas (scaling electrostatics)" help="Values must be between 0 and 1."/>
+               <param name="vdw"    type="text" value="0.00 0.04 0.08 0.11 0.15 0.19 0.23 0.27 0.30 0.34 0.38 0.42 0.46 0.49 0.53 0.57 0.61 0.65 0.68 0.72 0.76 0.80 0.84 0.87 0.91 0.95 0.97 0.98 0.99 0.999 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00" label="Van der Waals Lambdas (scaling vdw interactions)" help="Values must be between 0 and 1."/>
+               <param name="bonded" type="text" value="0.00 0.04 0.08 0.11 0.15 0.19 0.23 0.27 0.30 0.34 0.38 0.42 0.46 0.49 0.53 0.57 0.61 0.65 0.68 0.72 0.76 0.80 0.84 0.87 0.91 0.95 0.97 0.98 0.99 0.999 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00" label="Bonded Lambdas (scaling torsion)" help="Values must be between 0 and 1."/>
+            </when>
+        </conditional>
+        <conditional name="feoptions">
+            <param name="feop" type="select" label="Free energy variables">
+                <option value="default">Use default options</option>
+                <option value="modify">Modify default options</option>
+            </param>
+            <when value="default"/>
+            <when value="modify">
+            <param name="scalpha" type="float" value="0.5" label="The soft-core alpha parameter (sc-alpha)" />
+            <param name="scrpower" type="integer" value="6" label="The power of the radial term in the soft-core equation (sc-r-power)" />
+            <param name="scpower" type="integer" value="1" label="The power for lambda in the soft-core function (sc-power)" />
+            <param name="sccoul" type="text" value="no" label="Apply the soft-core free energy interaction transformation to the Columbic interaction of a molecule (sc-coul)? "/>
+            <param name="scsigma" type="float" value="0.3" label="The soft-core sigma" />
+            <param name="couplelambda0" type="text" value="vdw-q" label="Interactions at lambda=0" help="options are vdw-q, vdw, q, or none"/>
+            <param name="couplelambda1" type="text" value="none" label="Interactions at lambda=1" help="options are vdw-q, vdw, q, or none"/>
+            <param name="coupleintramol" type="text" value="no" label="Turn off intra-molecular interactions?" />
+            </when>
+        </conditional>
+        <param name="temperature" type="float" value="300.0" label="Temperature /K" />
+        <param name="pressure" type="float" value="1.0" label="Pressure /bar" />
+        <param name="input_fep" type="select" label="Perform simulation or only generate input files?">
+            <option value="perform">Perform simulation</option>
+            <option value="generate">Only generate input files</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="fepinpout" format="tar" from_work_dir="input_files.tar" label="Input files">
+             <filter>input_fep == 'generate'</filter>
+        </data>
+        <data name="dataout" format="tar" from_work_dir="data.tar" label="TI/FEP data output">
+             <filter>input_fep == 'perform'</filter>
+        </data>
+        <data name="trajout" format="tar" from_work_dir="traj.tar" label="Trajectories output">
+             <filter>input_fep == 'perform'</filter>
+        </data>
+        <data name="report" format="txt" label="Report">
+             <filter>input_fep == 'perform'</filter>
+        </data>
+    </outputs>
+    <tests>
+         <test>
+            <param name="groin" value="morph.gro" ftype="gro"/>
+            <param name="topin" value="morph.top" ftype="top"/>
+            <param name="minstep" value="10"/>
+            <param name="nvtstep" value="50"/>
+            <param name="nptstep" value="50"/>
+            <param name="mdstep" value="100"/>
+            <param name="seed" value="19880924"/>
+            <param name="cons" value="no"/>
+            <param name="dt" value="0.001"/>
+            <param name="path" value="global"/>
+            <param name="lambda" value="2"/>
+            <param name="fep" value="0.00 0.50 1.00"/>
+            <param name="temperature" value="300.0"/>
+            <param name="fepop" value="default"/>
+            <param name="input_fep" value="perform"/>
+            <param name="pressure" value="1.0"/>
+            <output name="dataout" file="TI_FEP_data_output.tar" compare="sim_size"/>
+        </test>
+        <test>
+            <param name="groin" value="morph.gro" ftype="gro"/>
+            <param name="topin" value="morph.top" ftype="top"/>
+            <param name="minstep" value="10000"/>
+            <param name="nvtstep" value="500000"/>
+            <param name="nptstep" value="500000"/>
+            <param name="mdstep" value="1000000"/>
+            <param name="seed" value="123546"/>
+            <param name="cons" value="yes"/>
+            <param name="cons_type" value="h-bonds"/>
+            <param name="lincs_order" value="4"/>
+            <param name="lincs_iter" value="1"/>
+            <param name="incs_warnangle" value="30"/>
+            <param name="dt" value="0.002"/>
+            <param name="path" value="default2"/>
+            <param name="lambda" value="40"/>
+            <param name="coul" value="0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.000 0.00 0.11 0.22 0.33 0.44 0.56 0.67 0.78 0.89 1.00"/>
+            <param name="vdw" value="0.00 0.04 0.08 0.11 0.15 0.19 0.23 0.27 0.30 0.34 0.38 0.42 0.46 0.49 0.53 0.57 0.61 0.65 0.68 0.72 0.76 0.80 0.84 0.87 0.91 0.95 0.97 0.98 0.99 0.999 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00"/>
+            <param name="bonded" value="0.00 0.04 0.08 0.11 0.15 0.19 0.23 0.27 0.30 0.34 0.38 0.42 0.46 0.49 0.53 0.57 0.61 0.65 0.68 0.72 0.76 0.80 0.84 0.87 0.91 0.95 0.97 0.98 0.99 0.999 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00"/>
+            <param name="temperature" value="300.0"/>
+            <param name="fepop" value="default"/>
+            <param name="input_fep" value="generate"/>
+            <param name="pressure" value="1.0"/>
+            <output name="fepinpout" file="Input_files.tar" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+
+    - This tool can run the alchemical free energy calculations using GROMACS.
+    - For more details about alchemical free energy calculations see http://www.alchemistry.org/wiki/Main_Page
+    - For details about GROMACS simulations see http://manual.gromacs.org/documentation/2019-rc1/user-guide/mdp-options.html
+
+When you need to run the simulation outside Galaxy, you can generate and down load all the input files from this tool.
+
+1. Simply download the output "Input files".
+2. Untar it using tar -xvf  Galaxy3-\[Input_files\].tar
+3. Run the bash script inside ./gmx_fep.sh {number of FEP windows}
+   - Give the number of FEP windows as an argument.
+
+This will generate input .MDP files and run all the steps for all the FEP windows iteratively.
+
+
+_____
+
+
+.. class:: infomark
+
+**Rules of Thumb for Intermediate States (taken from alchemistry.org)**
+
+    - These rules are not the end-all set and you should be familiar with why each one is suggested before just accepting them.
+    - Bonded terms can be modified/turned off linearly. This includes angle or bond force constants as well as unconstrained bond distances.
+    - Constrained bonds should not change length. There are free energy changes that cannot be ignored affiliated with this action.
+    - Maximize similarity between states by removing/decoupling as few atoms as possible.
+    - Do not open and close rings. This supersedes the previous rule.
+    - Statistical uncertainty between any neighboring states should be equal. Rather challenging to do, but it has been proven to have the lowest variance path if you can pull it off.
+    - Deleting or adding atoms should always be done with a soft core potential.
+    - Changes in parameters can be done linearly.
+    - All charge on atoms must be turned off prior to atomic repulsion. Otherwise you can get an infinite attractive potential and crash your simulation.
+    - Similarly for only changes in terms, it's generally more efficient to change electrostatic terms separate from Lennard-Jones terms.
+    - More states is better than fewer. Variance shrinks rapidly with number of states. You want the difference between intermediaries to be between 2-3 kBT
+
+Obviously you will be limited on CPU power. Fewer states also leads to more samples begin required from each state, so take this into account when deciding number of states as well.
+However, for MBAR and TI, it can be shown that spreading samples across multiple states does not significantly affect the uncertainty, since for TI, each state contributes less to
+the total uncertainty, and in MBAR, data contributes to the statistical precision of states with similar values of lambda.
+
+Shape of the variance does not significantly change with number of atoms, only magnitude. More intermediates will still be required for a large number of atoms to reduce statistical noise.
+Charge should be maintained across all λ
+
+Simply having charged molecules is fine, but the net of the system should remain constant. If you must change the net charge, there are complicated ways to do so.
+
+Short prototype simulations are recommended. Even as short as 100 ps, the prototypes can provide rough magnitude of variance estimates,
+although will likely under-predict the free energy as many configurations remain unsampled.
+
+
+_____
+
+
+.. class:: infomark
+
+**Input**
+
+       - .GRO input
+       - .TOP input
+
+_____
+
+
+.. class:: infomark
+
+**Output**
+
+       - TI/FEP data
+       - TI/FEP trajectory
+       - Report
+
+    ]]></help>
+    <citations>
+       <citation type="doi">10.1016/j.softx.2015.06.001</citation>
+      <citation type="bibtex">@misc{alchemistrywiki, title={Alchemistry.org}, url={http://www.alchemistry.org/wiki/Main_Page}, journal={AlchemistryWiki}}
+      </citation>
+    </citations>
+</tool>
Binary file alchemical_run/test-data/Input_files.tar has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alchemical_run/test-data/Report.txt	Mon Nov 11 13:20:39 2019 -0500
@@ -0,0 +1,1636 @@
+Starting minimization for lambda = 0...
+                      :-) GROMACS - gmx grompp, 2019.1 (-:
+
+                            GROMACS is written by:
+     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
+    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd
+ Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray
+  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang
+  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
+    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson
+  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund
+    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall
+    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov
+   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen
+ Christian Wennberg    Maarten Wolf
+                           and the project leaders:
+        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
+
+Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+Copyright (c) 2001-2018, The GROMACS development team at
+Uppsala University, Stockholm University and
+the Royal Institute of Technology, Sweden.
+check out http://www.gromacs.org for more information.
+
+GROMACS is free software; you can redistribute it and/or modify it
+under the terms of the GNU Lesser General Public License
+as published by the Free Software Foundation; either version 2.1
+of the License, or (at your option) any later version.
+
+GROMACS:      gmx grompp, version 2019.1
+Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
+Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
+Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/EM
+Command line:
+  gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/em_steep_0.mdp -c /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -o min0.tpr
+
+Setting the LD random seed to -127141127
+Generated 45 of the 45 non-bonded parameter combinations
+Generating 1-4 interactions: fudge = 0.5
+Generated 45 of the 45 1-4 parameter combinations
+Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
+Excluding 3 bonded neighbours molecule type 'NA'
+Excluding 3 bonded neighbours molecule type 'CL'
+Excluding 3 bonded neighbours molecule type 'WAT'
+Removing all charge groups because cutoff-scheme=Verlet
+Number of degrees of freedom in T-Coupling group rest is 12987.00
+Estimate for the relative computational load of the PME mesh part: 0.21
+
+GROMACS reminds you: "Wedged as we are between two eternities of idleness, there is no excuse for being idle now" (Anthony Burgess)
+
+Analysing residue names:
+There are:     1      Other residues
+There are:    10        Ion residues
+There are:  2151      Water residues
+Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
+Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
+Calculating fourier grid dimensions for X Y Z
+Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
+This run will generate roughly 1 Mb of data
+                      :-) GROMACS - gmx mdrun, 2019.1 (-:
+
+                            GROMACS is written by:
+     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
+    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd
+ Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray
+  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang
+  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
+    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson
+  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund
+    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall
+    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov
+   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen
+ Christian Wennberg    Maarten Wolf
+                           and the project leaders:
+        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
+
+Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+Copyright (c) 2001-2018, The GROMACS development team at
+Uppsala University, Stockholm University and
+the Royal Institute of Technology, Sweden.
+check out http://www.gromacs.org for more information.
+
+GROMACS is free software; you can redistribute it and/or modify it
+under the terms of the GNU Lesser General Public License
+as published by the Free Software Foundation; either version 2.1
+of the License, or (at your option) any later version.
+
+GROMACS:      gmx mdrun, version 2019.1
+Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
+Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
+Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/EM
+Command line:
+  gmx mdrun -deffnm min0
+
+Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
+The current CPU can measure timings more accurately than the code in
+gmx mdrun was configured to use. This might affect your simulation
+speed as accurate timings are needed for load-balancing.
+Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
+Reading file min0.tpr, VERSION 2019.1 (single precision)
+
+Using 1 MPI thread
+Using 4 OpenMP threads
+
+
+Steepest Descents:
+   Tolerance (Fmax)   =  1.00000e+02
+   Number of steps    =           10
+
+Energy minimization reached the maximum number of steps before the forces
+reached the requested precision Fmax < 100.
+
+writing lowest energy coordinates.
+
+Steepest Descents did not converge to Fmax < 100 in 11 steps.
+Potential Energy  = -8.3125391e+04
+Maximum force     =  2.1372287e+04 on atom 1
+Norm of force     =  5.1859150e+02
+
+GROMACS reminds you: "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material." (Watson & Crick)
+
+Starting constant volume equilibration...
+                      :-) GROMACS - gmx grompp, 2019.1 (-:
+
+                            GROMACS is written by:
+     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
+    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd
+ Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray
+  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang
+  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
+    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson
+  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund
+    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall
+    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov
+   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen
+ Christian Wennberg    Maarten Wolf
+                           and the project leaders:
+        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
+
+Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+Copyright (c) 2001-2018, The GROMACS development team at
+Uppsala University, Stockholm University and
+the Royal Institute of Technology, Sweden.
+check out http://www.gromacs.org for more information.
+
+GROMACS is free software; you can redistribute it and/or modify it
+under the terms of the GNU Lesser General Public License
+as published by the Free Software Foundation; either version 2.1
+of the License, or (at your option) any later version.
+
+GROMACS:      gmx grompp, version 2019.1
+Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
+Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
+Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/NVT
+Command line:
+  gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/nvt_0.mdp -c ../EM/min0.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -o nvt0.tpr
+
+Setting the LD random seed to -187712966
+Generated 45 of the 45 non-bonded parameter combinations
+Generating 1-4 interactions: fudge = 0.5
+Generated 45 of the 45 1-4 parameter combinations
+Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
+Excluding 3 bonded neighbours molecule type 'NA'
+Excluding 3 bonded neighbours molecule type 'CL'
+Excluding 3 bonded neighbours molecule type 'WAT'
+Velocities were taken from a Maxwell distribution at 300 K
+Removing all charge groups because cutoff-scheme=Verlet
+
+NOTE 1 [file morph.top, line 232]:
+  The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
+  an estimated oscillational period of 8.0e-03 ps, which is less than 10
+  times the time step of 1.0e-03 ps.
+  Maybe you forgot to change the constraints mdp option.
+
+Number of degrees of freedom in T-Coupling group System is 12987.00
+Estimate for the relative computational load of the PME mesh part: 0.23
+
+There was 1 note
+
+GROMACS reminds you: "Nada e organico, e tudo programado" (Pitty)
+
+Analysing residue names:
+There are:     1      Other residues
+There are:    10        Ion residues
+There are:  2151      Water residues
+Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
+Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
+Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
+Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm
+Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm
+Note that mdrun will redetermine rlist based on the actual pair-list setup
+Calculating fourier grid dimensions for X Y Z
+Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
+This run will generate roughly 1 Mb of data
+                      :-) GROMACS - gmx mdrun, 2019.1 (-:
+
+                            GROMACS is written by:
+     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
+    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd
+ Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray
+  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang
+  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
+    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson
+  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund
+    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall
+    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov
+   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen
+ Christian Wennberg    Maarten Wolf
+                           and the project leaders:
+        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
+
+Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+Copyright (c) 2001-2018, The GROMACS development team at
+Uppsala University, Stockholm University and
+the Royal Institute of Technology, Sweden.
+check out http://www.gromacs.org for more information.
+
+GROMACS is free software; you can redistribute it and/or modify it
+under the terms of the GNU Lesser General Public License
+as published by the Free Software Foundation; either version 2.1
+of the License, or (at your option) any later version.
+
+GROMACS:      gmx mdrun, version 2019.1
+Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
+Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
+Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/NVT
+Command line:
+  gmx mdrun -deffnm nvt0
+
+Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
+The current CPU can measure timings more accurately than the code in
+gmx mdrun was configured to use. This might affect your simulation
+speed as accurate timings are needed for load-balancing.
+Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
+Reading file nvt0.tpr, VERSION 2019.1 (single precision)
+Changing nstlist from 20 to 100, rlist from 1.2 to 1.2
+
+
+Using 1 MPI thread
+Using 4 OpenMP threads
+
+starting mdrun 'BioSimSpace System'
+50 steps,      0.1 ps.
+
+Writing final coordinates.
+
+               Core t (s)   Wall t (s)        (%)
+       Time:        1.458        0.365      399.9
+                 (ns/day)    (hour/ns)
+Performance:       12.084        1.986
+
+GROMACS reminds you: "I Quit My Job Blowing Leaves" (Beck)
+
+Constant volume equilibration complete.
+Starting constant pressure equilibration...
+                      :-) GROMACS - gmx grompp, 2019.1 (-:
+
+                            GROMACS is written by:
+     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
+    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd
+ Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray
+  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang
+  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
+    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson
+  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund
+    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall
+    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov
+   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen
+ Christian Wennberg    Maarten Wolf
+                           and the project leaders:
+        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
+
+Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+Copyright (c) 2001-2018, The GROMACS development team at
+Uppsala University, Stockholm University and
+the Royal Institute of Technology, Sweden.
+check out http://www.gromacs.org for more information.
+
+GROMACS is free software; you can redistribute it and/or modify it
+under the terms of the GNU Lesser General Public License
+as published by the Free Software Foundation; either version 2.1
+of the License, or (at your option) any later version.
+
+GROMACS:      gmx grompp, version 2019.1
+Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
+Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
+Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/NPT
+Command line:
+  gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/npt_0.mdp -c ../NVT/nvt0.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -t ../NVT/nvt0.cpt -o npt0.tpr
+
+Setting the LD random seed to 2038796930
+Generated 45 of the 45 non-bonded parameter combinations
+Generating 1-4 interactions: fudge = 0.5
+Generated 45 of the 45 1-4 parameter combinations
+Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
+Excluding 3 bonded neighbours molecule type 'NA'
+Excluding 3 bonded neighbours molecule type 'CL'
+Excluding 3 bonded neighbours molecule type 'WAT'
+Removing all charge groups because cutoff-scheme=Verlet
+
+NOTE 1 [file morph.top, line 232]:
+  The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
+  an estimated oscillational period of 8.0e-03 ps, which is less than 10
+  times the time step of 1.0e-03 ps.
+  Maybe you forgot to change the constraints mdp option.
+
+Number of degrees of freedom in T-Coupling group System is 12987.00
+Reading Coordinates, Velocities and Box size from old trajectory
+Will read whole trajectory
+
Last frame         -1 time    0.050
+Using frame at t = 0.05 ps
+Starting time for run is 0 ps
+Estimate for the relative computational load of the PME mesh part: 0.23
+
+There was 1 note
+
+GROMACS reminds you: "Act like Prometheus would" (Gogol Bordello)
+
+Analysing residue names:
+There are:     1      Other residues
+There are:    10        Ion residues
+There are:  2151      Water residues
+Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
+Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
+Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
+Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm
+Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm
+Note that mdrun will redetermine rlist based on the actual pair-list setup
+Calculating fourier grid dimensions for X Y Z
+Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
+This run will generate roughly 1 Mb of data
+                      :-) GROMACS - gmx mdrun, 2019.1 (-:
+
+                            GROMACS is written by:
+     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
+    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd
+ Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray
+  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang
+  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
+    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson
+  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund
+    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall
+    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov
+   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen
+ Christian Wennberg    Maarten Wolf
+                           and the project leaders:
+        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
+
+Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+Copyright (c) 2001-2018, The GROMACS development team at
+Uppsala University, Stockholm University and
+the Royal Institute of Technology, Sweden.
+check out http://www.gromacs.org for more information.
+
+GROMACS is free software; you can redistribute it and/or modify it
+under the terms of the GNU Lesser General Public License
+as published by the Free Software Foundation; either version 2.1
+of the License, or (at your option) any later version.
+
+GROMACS:      gmx mdrun, version 2019.1
+Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
+Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
+Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/NPT
+Command line:
+  gmx mdrun -deffnm npt0
+
+Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
+The current CPU can measure timings more accurately than the code in
+gmx mdrun was configured to use. This might affect your simulation
+speed as accurate timings are needed for load-balancing.
+Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
+Reading file npt0.tpr, VERSION 2019.1 (single precision)
+Changing nstlist from 20 to 100, rlist from 1.2 to 1.2
+
+
+Using 1 MPI thread
+Using 4 OpenMP threads
+
+starting mdrun 'BioSimSpace System'
+50 steps,      0.1 ps.
+
+Writing final coordinates.
+
+               Core t (s)   Wall t (s)        (%)
+       Time:        1.261        0.315      399.9
+                 (ns/day)    (hour/ns)
+Performance:       13.979        1.717
+
+GROMACS reminds you: "I Was Born to Have Adventure" (F. Zappa)
+
+Constant pressure equilibration complete.
+Starting production MD simulation...
+                      :-) GROMACS - gmx grompp, 2019.1 (-:
+
+                            GROMACS is written by:
+     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
+    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd
+ Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray
+  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang
+  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
+    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson
+  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund
+    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall
+    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov
+   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen
+ Christian Wennberg    Maarten Wolf
+                           and the project leaders:
+        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
+
+Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+Copyright (c) 2001-2018, The GROMACS development team at
+Uppsala University, Stockholm University and
+the Royal Institute of Technology, Sweden.
+check out http://www.gromacs.org for more information.
+
+GROMACS is free software; you can redistribute it and/or modify it
+under the terms of the GNU Lesser General Public License
+as published by the Free Software Foundation; either version 2.1
+of the License, or (at your option) any later version.
+
+GROMACS:      gmx grompp, version 2019.1
+Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
+Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
+Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/Production_MD
+Command line:
+  gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_0.mdp -c ../NPT/npt0.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -t ../NPT/npt0.cpt -o md0.tpr
+
+
+NOTE 1 [file /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_0.mdp]:
+  With PME there is a minor soft core effect present at the cut-off,
+  proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on
+  energy conservation, but usually other effects dominate. With a common
+  sigma value of 0.34 nm the fraction of the particle-particle potential at
+  the cut-off at lambda=0.5 is around 2.5e-04, while ewald-rtol is 1.0e-05.
+
+Setting the LD random seed to -1773803540
+Generated 45 of the 45 non-bonded parameter combinations
+Generating 1-4 interactions: fudge = 0.5
+Generated 45 of the 45 1-4 parameter combinations
+Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
+Excluding 3 bonded neighbours molecule type 'NA'
+Excluding 3 bonded neighbours molecule type 'CL'
+Excluding 3 bonded neighbours molecule type 'WAT'
+Removing all charge groups because cutoff-scheme=Verlet
+
+NOTE 2 [file morph.top, line 232]:
+  The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
+  an estimated oscillational period of 8.0e-03 ps, which is less than 10
+  times the time step of 1.0e-03 ps.
+  Maybe you forgot to change the constraints mdp option.
+
+Number of degrees of freedom in T-Coupling group System is 12987.00
+Reading Coordinates, Velocities and Box size from old trajectory
+Will read whole trajectory
+
Last frame         -1 time    0.050
+Using frame at t = 0.05 ps
+Starting time for run is 0 ps
+Estimate for the relative computational load of the PME mesh part: 0.47
+
+There were 2 notes
+
+GROMACS reminds you: "God is a DJ" (Faithless)
+
+Analysing residue names:
+There are:     1      Other residues
+There are:    10        Ion residues
+There are:  2151      Water residues
+Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
+Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
+Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
+Calculated rlist for 1x1 atom pair-list as 0.812 nm, buffer size 0.012 nm
+Set rlist, assuming 4x4 atom pair-list, to 0.800 nm, buffer size 0.000 nm
+Note that mdrun will redetermine rlist based on the actual pair-list setup
+Calculating fourier grid dimensions for X Y Z
+Using a fourier grid of 42x42x42, spacing 0.096 0.096 0.096
+This run will generate roughly 1 Mb of data
+                      :-) GROMACS - gmx mdrun, 2019.1 (-:
+
+                            GROMACS is written by:
+     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
+    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd
+ Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray
+  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang
+  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
+    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson
+  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund
+    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall
+    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov
+   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen
+ Christian Wennberg    Maarten Wolf
+                           and the project leaders:
+        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
+
+Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+Copyright (c) 2001-2018, The GROMACS development team at
+Uppsala University, Stockholm University and
+the Royal Institute of Technology, Sweden.
+check out http://www.gromacs.org for more information.
+
+GROMACS is free software; you can redistribute it and/or modify it
+under the terms of the GNU Lesser General Public License
+as published by the Free Software Foundation; either version 2.1
+of the License, or (at your option) any later version.
+
+GROMACS:      gmx mdrun, version 2019.1
+Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
+Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
+Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_0/Production_MD
+Command line:
+  gmx mdrun -deffnm md0
+
+Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
+The current CPU can measure timings more accurately than the code in
+gmx mdrun was configured to use. This might affect your simulation
+speed as accurate timings are needed for load-balancing.
+Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
+Reading file md0.tpr, VERSION 2019.1 (single precision)
+Changing nstlist from 10 to 50, rlist from 0.8 to 0.86
+
+
+Using 1 MPI thread
+Using 4 OpenMP threads
+
+starting mdrun 'BioSimSpace System'
+2000 steps,      2.0 ps.
+
+Writing final coordinates.
+
+               Core t (s)   Wall t (s)        (%)
+       Time:       27.033        6.758      400.0
+                 (ns/day)    (hour/ns)
+Performance:       25.581        0.938
+
+GROMACS reminds you: "Don't You Wish You Never Met Her, Dirty Blue Gene?" (Captain Beefheart)
+
+Production MD complete.
+Ending. Job completed for lambda = 0
+Starting minimization for lambda = 1...
+                      :-) GROMACS - gmx grompp, 2019.1 (-:
+
+                            GROMACS is written by:
+     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
+    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd
+ Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray
+  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang
+  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
+    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson
+  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund
+    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall
+    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov
+   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen
+ Christian Wennberg    Maarten Wolf
+                           and the project leaders:
+        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
+
+Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+Copyright (c) 2001-2018, The GROMACS development team at
+Uppsala University, Stockholm University and
+the Royal Institute of Technology, Sweden.
+check out http://www.gromacs.org for more information.
+
+GROMACS is free software; you can redistribute it and/or modify it
+under the terms of the GNU Lesser General Public License
+as published by the Free Software Foundation; either version 2.1
+of the License, or (at your option) any later version.
+
+GROMACS:      gmx grompp, version 2019.1
+Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
+Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
+Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/EM
+Command line:
+  gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/em_steep_1.mdp -c /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -o min1.tpr
+
+Setting the LD random seed to -1393309481
+Generated 45 of the 45 non-bonded parameter combinations
+Generating 1-4 interactions: fudge = 0.5
+Generated 45 of the 45 1-4 parameter combinations
+Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
+Excluding 3 bonded neighbours molecule type 'NA'
+Excluding 3 bonded neighbours molecule type 'CL'
+Excluding 3 bonded neighbours molecule type 'WAT'
+Removing all charge groups because cutoff-scheme=Verlet
+Number of degrees of freedom in T-Coupling group rest is 12987.00
+Estimate for the relative computational load of the PME mesh part: 0.21
+
+GROMACS reminds you: "Scientists think they are born with logic; God forbid they should study this discipline with a history of more than two and a half millennia." (Roald Hoffmann)
+
+Analysing residue names:
+There are:     1      Other residues
+There are:    10        Ion residues
+There are:  2151      Water residues
+Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
+Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
+Calculating fourier grid dimensions for X Y Z
+Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
+This run will generate roughly 1 Mb of data
+                      :-) GROMACS - gmx mdrun, 2019.1 (-:
+
+                            GROMACS is written by:
+     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
+    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd
+ Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray
+  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang
+  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
+    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson
+  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund
+    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall
+    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov
+   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen
+ Christian Wennberg    Maarten Wolf
+                           and the project leaders:
+        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
+
+Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+Copyright (c) 2001-2018, The GROMACS development team at
+Uppsala University, Stockholm University and
+the Royal Institute of Technology, Sweden.
+check out http://www.gromacs.org for more information.
+
+GROMACS is free software; you can redistribute it and/or modify it
+under the terms of the GNU Lesser General Public License
+as published by the Free Software Foundation; either version 2.1
+of the License, or (at your option) any later version.
+
+GROMACS:      gmx mdrun, version 2019.1
+Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
+Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
+Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/EM
+Command line:
+  gmx mdrun -deffnm min1
+
+Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
+The current CPU can measure timings more accurately than the code in
+gmx mdrun was configured to use. This might affect your simulation
+speed as accurate timings are needed for load-balancing.
+Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
+Reading file min1.tpr, VERSION 2019.1 (single precision)
+
+Using 1 MPI thread
+Using 4 OpenMP threads
+
+
+Steepest Descents:
+   Tolerance (Fmax)   =  1.00000e+02
+   Number of steps    =           10
+
+Energy minimization reached the maximum number of steps before the forces
+reached the requested precision Fmax < 100.
+
+writing lowest energy coordinates.
+
+Steepest Descents did not converge to Fmax < 100 in 11 steps.
+Potential Energy  = -8.3125391e+04
+Maximum force     =  2.1372287e+04 on atom 1
+Norm of force     =  5.1859150e+02
+
+GROMACS reminds you: "Der Ball ist rund, das Spiel dauert 90 minuten, alles andere ist Theorie" (Lola rennt)
+
+Starting constant volume equilibration...
+                      :-) GROMACS - gmx grompp, 2019.1 (-:
+
+                            GROMACS is written by:
+     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
+    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd
+ Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray
+  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang
+  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
+    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson
+  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund
+    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall
+    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov
+   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen
+ Christian Wennberg    Maarten Wolf
+                           and the project leaders:
+        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
+
+Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+Copyright (c) 2001-2018, The GROMACS development team at
+Uppsala University, Stockholm University and
+the Royal Institute of Technology, Sweden.
+check out http://www.gromacs.org for more information.
+
+GROMACS is free software; you can redistribute it and/or modify it
+under the terms of the GNU Lesser General Public License
+as published by the Free Software Foundation; either version 2.1
+of the License, or (at your option) any later version.
+
+GROMACS:      gmx grompp, version 2019.1
+Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
+Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
+Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/NVT
+Command line:
+  gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/nvt_1.mdp -c ../EM/min1.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -o nvt1.tpr
+
+Setting the LD random seed to -1631510067
+Generated 45 of the 45 non-bonded parameter combinations
+Generating 1-4 interactions: fudge = 0.5
+Generated 45 of the 45 1-4 parameter combinations
+Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
+Excluding 3 bonded neighbours molecule type 'NA'
+Excluding 3 bonded neighbours molecule type 'CL'
+Excluding 3 bonded neighbours molecule type 'WAT'
+Velocities were taken from a Maxwell distribution at 300 K
+Removing all charge groups because cutoff-scheme=Verlet
+
+NOTE 1 [file morph.top, line 232]:
+  The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
+  an estimated oscillational period of 8.0e-03 ps, which is less than 10
+  times the time step of 1.0e-03 ps.
+  Maybe you forgot to change the constraints mdp option.
+
+Number of degrees of freedom in T-Coupling group System is 12987.00
+Estimate for the relative computational load of the PME mesh part: 0.23
+
+There was 1 note
+
+GROMACS reminds you: "No great discovery was ever made without a bold guess." (Marie Curie)
+
+Analysing residue names:
+There are:     1      Other residues
+There are:    10        Ion residues
+There are:  2151      Water residues
+Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
+Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
+Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
+Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm
+Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm
+Note that mdrun will redetermine rlist based on the actual pair-list setup
+Calculating fourier grid dimensions for X Y Z
+Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
+This run will generate roughly 1 Mb of data
+                      :-) GROMACS - gmx mdrun, 2019.1 (-:
+
+                            GROMACS is written by:
+     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
+    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd
+ Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray
+  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang
+  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
+    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson
+  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund
+    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall
+    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov
+   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen
+ Christian Wennberg    Maarten Wolf
+                           and the project leaders:
+        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
+
+Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+Copyright (c) 2001-2018, The GROMACS development team at
+Uppsala University, Stockholm University and
+the Royal Institute of Technology, Sweden.
+check out http://www.gromacs.org for more information.
+
+GROMACS is free software; you can redistribute it and/or modify it
+under the terms of the GNU Lesser General Public License
+as published by the Free Software Foundation; either version 2.1
+of the License, or (at your option) any later version.
+
+GROMACS:      gmx mdrun, version 2019.1
+Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
+Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
+Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/NVT
+Command line:
+  gmx mdrun -deffnm nvt1
+
+Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
+The current CPU can measure timings more accurately than the code in
+gmx mdrun was configured to use. This might affect your simulation
+speed as accurate timings are needed for load-balancing.
+Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
+Reading file nvt1.tpr, VERSION 2019.1 (single precision)
+Changing nstlist from 20 to 100, rlist from 1.2 to 1.2
+
+
+Using 1 MPI thread
+Using 4 OpenMP threads
+
+starting mdrun 'BioSimSpace System'
+50 steps,      0.1 ps.
+
+Writing final coordinates.
+
+               Core t (s)   Wall t (s)        (%)
+       Time:        1.273        0.318      399.9
+                 (ns/day)    (hour/ns)
+Performance:       13.842        1.734
+
+GROMACS reminds you: "You're like them scientists on TV explaining black holes. More you talk, less I get" (Jess Walter)
+
+Constant volume equilibration complete.
+Starting constant pressure equilibration...
+                      :-) GROMACS - gmx grompp, 2019.1 (-:
+
+                            GROMACS is written by:
+     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
+    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd
+ Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray
+  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang
+  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
+    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson
+  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund
+    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall
+    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov
+   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen
+ Christian Wennberg    Maarten Wolf
+                           and the project leaders:
+        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
+
+Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+Copyright (c) 2001-2018, The GROMACS development team at
+Uppsala University, Stockholm University and
+the Royal Institute of Technology, Sweden.
+check out http://www.gromacs.org for more information.
+
+GROMACS is free software; you can redistribute it and/or modify it
+under the terms of the GNU Lesser General Public License
+as published by the Free Software Foundation; either version 2.1
+of the License, or (at your option) any later version.
+
+GROMACS:      gmx grompp, version 2019.1
+Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
+Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
+Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/NPT
+Command line:
+  gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/npt_1.mdp -c ../NVT/nvt1.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -t ../NVT/nvt1.cpt -o npt1.tpr
+
+Setting the LD random seed to -166230178
+Generated 45 of the 45 non-bonded parameter combinations
+Generating 1-4 interactions: fudge = 0.5
+Generated 45 of the 45 1-4 parameter combinations
+Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
+Excluding 3 bonded neighbours molecule type 'NA'
+Excluding 3 bonded neighbours molecule type 'CL'
+Excluding 3 bonded neighbours molecule type 'WAT'
+Removing all charge groups because cutoff-scheme=Verlet
+
+NOTE 1 [file morph.top, line 232]:
+  The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
+  an estimated oscillational period of 8.0e-03 ps, which is less than 10
+  times the time step of 1.0e-03 ps.
+  Maybe you forgot to change the constraints mdp option.
+
+Number of degrees of freedom in T-Coupling group System is 12987.00
+Reading Coordinates, Velocities and Box size from old trajectory
+Will read whole trajectory
+
Last frame         -1 time    0.050
+Using frame at t = 0.05 ps
+Starting time for run is 0 ps
+Estimate for the relative computational load of the PME mesh part: 0.23
+
+There was 1 note
+
+GROMACS reminds you: "Keep Your Shoes and Socks On, People" (F. Zappa)
+
+Analysing residue names:
+There are:     1      Other residues
+There are:    10        Ion residues
+There are:  2151      Water residues
+Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
+Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
+Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
+Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm
+Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm
+Note that mdrun will redetermine rlist based on the actual pair-list setup
+Calculating fourier grid dimensions for X Y Z
+Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
+This run will generate roughly 1 Mb of data
+                      :-) GROMACS - gmx mdrun, 2019.1 (-:
+
+                            GROMACS is written by:
+     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
+    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd
+ Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray
+  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang
+  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
+    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson
+  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund
+    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall
+    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov
+   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen
+ Christian Wennberg    Maarten Wolf
+                           and the project leaders:
+        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
+
+Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+Copyright (c) 2001-2018, The GROMACS development team at
+Uppsala University, Stockholm University and
+the Royal Institute of Technology, Sweden.
+check out http://www.gromacs.org for more information.
+
+GROMACS is free software; you can redistribute it and/or modify it
+under the terms of the GNU Lesser General Public License
+as published by the Free Software Foundation; either version 2.1
+of the License, or (at your option) any later version.
+
+GROMACS:      gmx mdrun, version 2019.1
+Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
+Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
+Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/NPT
+Command line:
+  gmx mdrun -deffnm npt1
+
+Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
+The current CPU can measure timings more accurately than the code in
+gmx mdrun was configured to use. This might affect your simulation
+speed as accurate timings are needed for load-balancing.
+Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
+Reading file npt1.tpr, VERSION 2019.1 (single precision)
+Changing nstlist from 20 to 100, rlist from 1.2 to 1.2
+
+
+Using 1 MPI thread
+Using 4 OpenMP threads
+
+starting mdrun 'BioSimSpace System'
+50 steps,      0.1 ps.
+
+Writing final coordinates.
+
+               Core t (s)   Wall t (s)        (%)
+       Time:        1.310        0.328      399.9
+                 (ns/day)    (hour/ns)
+Performance:       13.448        1.785
+
+GROMACS reminds you: "Don't Follow Me Home" (Throwing Muses)
+
+Constant pressure equilibration complete.
+Starting production MD simulation...
+                      :-) GROMACS - gmx grompp, 2019.1 (-:
+
+                            GROMACS is written by:
+     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
+    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd
+ Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray
+  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang
+  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
+    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson
+  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund
+    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall
+    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov
+   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen
+ Christian Wennberg    Maarten Wolf
+                           and the project leaders:
+        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
+
+Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+Copyright (c) 2001-2018, The GROMACS development team at
+Uppsala University, Stockholm University and
+the Royal Institute of Technology, Sweden.
+check out http://www.gromacs.org for more information.
+
+GROMACS is free software; you can redistribute it and/or modify it
+under the terms of the GNU Lesser General Public License
+as published by the Free Software Foundation; either version 2.1
+of the License, or (at your option) any later version.
+
+GROMACS:      gmx grompp, version 2019.1
+Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
+Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
+Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/Production_MD
+Command line:
+  gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_1.mdp -c ../NPT/npt1.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -t ../NPT/npt1.cpt -o md1.tpr
+
+
+NOTE 1 [file /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_1.mdp]:
+  With PME there is a minor soft core effect present at the cut-off,
+  proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on
+  energy conservation, but usually other effects dominate. With a common
+  sigma value of 0.34 nm the fraction of the particle-particle potential at
+  the cut-off at lambda=0.5 is around 2.5e-04, while ewald-rtol is 1.0e-05.
+
+Setting the LD random seed to -651728442
+Generated 45 of the 45 non-bonded parameter combinations
+Generating 1-4 interactions: fudge = 0.5
+Generated 45 of the 45 1-4 parameter combinations
+Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
+Excluding 3 bonded neighbours molecule type 'NA'
+Excluding 3 bonded neighbours molecule type 'CL'
+Excluding 3 bonded neighbours molecule type 'WAT'
+Removing all charge groups because cutoff-scheme=Verlet
+
+NOTE 2 [file morph.top, line 232]:
+  The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
+  an estimated oscillational period of 8.0e-03 ps, which is less than 10
+  times the time step of 1.0e-03 ps.
+  Maybe you forgot to change the constraints mdp option.
+
+Number of degrees of freedom in T-Coupling group System is 12987.00
+Reading Coordinates, Velocities and Box size from old trajectory
+Will read whole trajectory
+
Last frame         -1 time    0.050
+Using frame at t = 0.05 ps
+Starting time for run is 0 ps
+Estimate for the relative computational load of the PME mesh part: 0.47
+
+There were 2 notes
+
+GROMACS reminds you: "Beat On the Brat With a Baseball Bat" (The Ramones)
+
+Analysing residue names:
+There are:     1      Other residues
+There are:    10        Ion residues
+There are:  2151      Water residues
+Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
+Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
+Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
+Calculated rlist for 1x1 atom pair-list as 0.812 nm, buffer size 0.012 nm
+Set rlist, assuming 4x4 atom pair-list, to 0.800 nm, buffer size 0.000 nm
+Note that mdrun will redetermine rlist based on the actual pair-list setup
+Calculating fourier grid dimensions for X Y Z
+Using a fourier grid of 42x42x42, spacing 0.096 0.096 0.096
+This run will generate roughly 1 Mb of data
+                      :-) GROMACS - gmx mdrun, 2019.1 (-:
+
+                            GROMACS is written by:
+     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
+    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd
+ Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray
+  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang
+  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
+    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson
+  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund
+    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall
+    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov
+   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen
+ Christian Wennberg    Maarten Wolf
+                           and the project leaders:
+        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
+
+Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+Copyright (c) 2001-2018, The GROMACS development team at
+Uppsala University, Stockholm University and
+the Royal Institute of Technology, Sweden.
+check out http://www.gromacs.org for more information.
+
+GROMACS is free software; you can redistribute it and/or modify it
+under the terms of the GNU Lesser General Public License
+as published by the Free Software Foundation; either version 2.1
+of the License, or (at your option) any later version.
+
+GROMACS:      gmx mdrun, version 2019.1
+Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
+Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
+Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_1/Production_MD
+Command line:
+  gmx mdrun -deffnm md1
+
+Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
+The current CPU can measure timings more accurately than the code in
+gmx mdrun was configured to use. This might affect your simulation
+speed as accurate timings are needed for load-balancing.
+Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
+Reading file md1.tpr, VERSION 2019.1 (single precision)
+Changing nstlist from 10 to 50, rlist from 0.8 to 0.86
+
+
+Using 1 MPI thread
+Using 4 OpenMP threads
+
+starting mdrun 'BioSimSpace System'
+2000 steps,      2.0 ps.
+
+Writing final coordinates.
+
+               Core t (s)   Wall t (s)        (%)
+       Time:       27.548        6.887      400.0
+                 (ns/day)    (hour/ns)
+Performance:       25.103        0.956
+
+GROMACS reminds you: "Nothing is more anarchic than power." (Pier Paolo Pasolini)
+
+Production MD complete.
+Ending. Job completed for lambda = 1
+Starting minimization for lambda = 2...
+                      :-) GROMACS - gmx grompp, 2019.1 (-:
+
+                            GROMACS is written by:
+     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
+    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd
+ Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray
+  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang
+  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
+    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson
+  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund
+    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall
+    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov
+   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen
+ Christian Wennberg    Maarten Wolf
+                           and the project leaders:
+        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
+
+Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+Copyright (c) 2001-2018, The GROMACS development team at
+Uppsala University, Stockholm University and
+the Royal Institute of Technology, Sweden.
+check out http://www.gromacs.org for more information.
+
+GROMACS is free software; you can redistribute it and/or modify it
+under the terms of the GNU Lesser General Public License
+as published by the Free Software Foundation; either version 2.1
+of the License, or (at your option) any later version.
+
+GROMACS:      gmx grompp, version 2019.1
+Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
+Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
+Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/EM
+Command line:
+  gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/em_steep_2.mdp -c /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -o min2.tpr
+
+Setting the LD random seed to 886887101
+Generated 45 of the 45 non-bonded parameter combinations
+Generating 1-4 interactions: fudge = 0.5
+Generated 45 of the 45 1-4 parameter combinations
+Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
+Excluding 3 bonded neighbours molecule type 'NA'
+Excluding 3 bonded neighbours molecule type 'CL'
+Excluding 3 bonded neighbours molecule type 'WAT'
+Removing all charge groups because cutoff-scheme=Verlet
+Number of degrees of freedom in T-Coupling group rest is 12987.00
+Estimate for the relative computational load of the PME mesh part: 0.21
+
+GROMACS reminds you: "Sisters Have Always Fascinated Me" (Speech)
+
+Analysing residue names:
+There are:     1      Other residues
+There are:    10        Ion residues
+There are:  2151      Water residues
+Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
+Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
+Calculating fourier grid dimensions for X Y Z
+Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
+This run will generate roughly 1 Mb of data
+                      :-) GROMACS - gmx mdrun, 2019.1 (-:
+
+                            GROMACS is written by:
+     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
+    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd
+ Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray
+  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang
+  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
+    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson
+  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund
+    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall
+    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov
+   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen
+ Christian Wennberg    Maarten Wolf
+                           and the project leaders:
+        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
+
+Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+Copyright (c) 2001-2018, The GROMACS development team at
+Uppsala University, Stockholm University and
+the Royal Institute of Technology, Sweden.
+check out http://www.gromacs.org for more information.
+
+GROMACS is free software; you can redistribute it and/or modify it
+under the terms of the GNU Lesser General Public License
+as published by the Free Software Foundation; either version 2.1
+of the License, or (at your option) any later version.
+
+GROMACS:      gmx mdrun, version 2019.1
+Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
+Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
+Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/EM
+Command line:
+  gmx mdrun -deffnm min2
+
+Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
+The current CPU can measure timings more accurately than the code in
+gmx mdrun was configured to use. This might affect your simulation
+speed as accurate timings are needed for load-balancing.
+Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
+Reading file min2.tpr, VERSION 2019.1 (single precision)
+
+Using 1 MPI thread
+Using 4 OpenMP threads
+
+
+Steepest Descents:
+   Tolerance (Fmax)   =  1.00000e+02
+   Number of steps    =           10
+
+Energy minimization reached the maximum number of steps before the forces
+reached the requested precision Fmax < 100.
+
+writing lowest energy coordinates.
+
+Steepest Descents did not converge to Fmax < 100 in 11 steps.
+Potential Energy  = -8.3125391e+04
+Maximum force     =  2.1372287e+04 on atom 1
+Norm of force     =  5.1859150e+02
+
+GROMACS reminds you: "The Candlelight Was Just Right" (Beastie Boys)
+
+Starting constant volume equilibration...
+                      :-) GROMACS - gmx grompp, 2019.1 (-:
+
+                            GROMACS is written by:
+     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
+    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd
+ Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray
+  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang
+  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
+    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson
+  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund
+    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall
+    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov
+   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen
+ Christian Wennberg    Maarten Wolf
+                           and the project leaders:
+        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
+
+Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+Copyright (c) 2001-2018, The GROMACS development team at
+Uppsala University, Stockholm University and
+the Royal Institute of Technology, Sweden.
+check out http://www.gromacs.org for more information.
+
+GROMACS is free software; you can redistribute it and/or modify it
+under the terms of the GNU Lesser General Public License
+as published by the Free Software Foundation; either version 2.1
+of the License, or (at your option) any later version.
+
+GROMACS:      gmx grompp, version 2019.1
+Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
+Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
+Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/NVT
+Command line:
+  gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/nvt_2.mdp -c ../EM/min2.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -o nvt2.tpr
+
+Setting the LD random seed to -902054215
+Generated 45 of the 45 non-bonded parameter combinations
+Generating 1-4 interactions: fudge = 0.5
+Generated 45 of the 45 1-4 parameter combinations
+Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
+Excluding 3 bonded neighbours molecule type 'NA'
+Excluding 3 bonded neighbours molecule type 'CL'
+Excluding 3 bonded neighbours molecule type 'WAT'
+Velocities were taken from a Maxwell distribution at 300 K
+Removing all charge groups because cutoff-scheme=Verlet
+
+NOTE 1 [file morph.top, line 232]:
+  The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
+  an estimated oscillational period of 8.0e-03 ps, which is less than 10
+  times the time step of 1.0e-03 ps.
+  Maybe you forgot to change the constraints mdp option.
+
+Number of degrees of freedom in T-Coupling group System is 12987.00
+Estimate for the relative computational load of the PME mesh part: 0.23
+
+There was 1 note
+
+GROMACS reminds you: "I spent a lot of money on booze, birds and fast cars. The rest I just squandered." (George Best)
+
+Analysing residue names:
+There are:     1      Other residues
+There are:    10        Ion residues
+There are:  2151      Water residues
+Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
+Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
+Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
+Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm
+Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm
+Note that mdrun will redetermine rlist based on the actual pair-list setup
+Calculating fourier grid dimensions for X Y Z
+Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
+This run will generate roughly 1 Mb of data
+                      :-) GROMACS - gmx mdrun, 2019.1 (-:
+
+                            GROMACS is written by:
+     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
+    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd
+ Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray
+  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang
+  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
+    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson
+  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund
+    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall
+    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov
+   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen
+ Christian Wennberg    Maarten Wolf
+                           and the project leaders:
+        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
+
+Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+Copyright (c) 2001-2018, The GROMACS development team at
+Uppsala University, Stockholm University and
+the Royal Institute of Technology, Sweden.
+check out http://www.gromacs.org for more information.
+
+GROMACS is free software; you can redistribute it and/or modify it
+under the terms of the GNU Lesser General Public License
+as published by the Free Software Foundation; either version 2.1
+of the License, or (at your option) any later version.
+
+GROMACS:      gmx mdrun, version 2019.1
+Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
+Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
+Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/NVT
+Command line:
+  gmx mdrun -deffnm nvt2
+
+Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
+The current CPU can measure timings more accurately than the code in
+gmx mdrun was configured to use. This might affect your simulation
+speed as accurate timings are needed for load-balancing.
+Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
+Reading file nvt2.tpr, VERSION 2019.1 (single precision)
+Changing nstlist from 20 to 100, rlist from 1.2 to 1.2
+
+
+Using 1 MPI thread
+Using 4 OpenMP threads
+
+starting mdrun 'BioSimSpace System'
+50 steps,      0.1 ps.
+
+Writing final coordinates.
+
+               Core t (s)   Wall t (s)        (%)
+       Time:        1.308        0.327      399.9
+                 (ns/day)    (hour/ns)
+Performance:       13.471        1.782
+
+GROMACS reminds you: "What if you're wrong about the great Ju Ju at the bottom of the sea?" (Richard Dawkins)
+
+Constant volume equilibration complete.
+Starting constant pressure equilibration...
+                      :-) GROMACS - gmx grompp, 2019.1 (-:
+
+                            GROMACS is written by:
+     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
+    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd
+ Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray
+  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang
+  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
+    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson
+  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund
+    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall
+    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov
+   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen
+ Christian Wennberg    Maarten Wolf
+                           and the project leaders:
+        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
+
+Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+Copyright (c) 2001-2018, The GROMACS development team at
+Uppsala University, Stockholm University and
+the Royal Institute of Technology, Sweden.
+check out http://www.gromacs.org for more information.
+
+GROMACS is free software; you can redistribute it and/or modify it
+under the terms of the GNU Lesser General Public License
+as published by the Free Software Foundation; either version 2.1
+of the License, or (at your option) any later version.
+
+GROMACS:      gmx grompp, version 2019.1
+Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
+Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
+Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/NPT
+Command line:
+  gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/npt_2.mdp -c ../NVT/nvt2.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -t ../NVT/nvt2.cpt -o npt2.tpr
+
+Setting the LD random seed to -652502066
+Generated 45 of the 45 non-bonded parameter combinations
+Generating 1-4 interactions: fudge = 0.5
+Generated 45 of the 45 1-4 parameter combinations
+Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
+Excluding 3 bonded neighbours molecule type 'NA'
+Excluding 3 bonded neighbours molecule type 'CL'
+Excluding 3 bonded neighbours molecule type 'WAT'
+Removing all charge groups because cutoff-scheme=Verlet
+
+NOTE 1 [file morph.top, line 232]:
+  The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
+  an estimated oscillational period of 8.0e-03 ps, which is less than 10
+  times the time step of 1.0e-03 ps.
+  Maybe you forgot to change the constraints mdp option.
+
+Number of degrees of freedom in T-Coupling group System is 12987.00
+Reading Coordinates, Velocities and Box size from old trajectory
+Will read whole trajectory
+
Last frame         -1 time    0.050
+Using frame at t = 0.05 ps
+Starting time for run is 0 ps
+Estimate for the relative computational load of the PME mesh part: 0.23
+
+There was 1 note
+
+GROMACS reminds you: "When doing HPC, don't communica" (Jim Demmel)
+
+Analysing residue names:
+There are:     1      Other residues
+There are:    10        Ion residues
+There are:  2151      Water residues
+Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
+Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
+Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
+Calculated rlist for 1x1 atom pair-list as 1.205 nm, buffer size 0.005 nm
+Set rlist, assuming 4x4 atom pair-list, to 1.200 nm, buffer size 0.000 nm
+Note that mdrun will redetermine rlist based on the actual pair-list setup
+Calculating fourier grid dimensions for X Y Z
+Using a fourier grid of 36x36x36, spacing 0.111 0.111 0.111
+This run will generate roughly 1 Mb of data
+                      :-) GROMACS - gmx mdrun, 2019.1 (-:
+
+                            GROMACS is written by:
+     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
+    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd
+ Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray
+  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang
+  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
+    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson
+  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund
+    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall
+    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov
+   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen
+ Christian Wennberg    Maarten Wolf
+                           and the project leaders:
+        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
+
+Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+Copyright (c) 2001-2018, The GROMACS development team at
+Uppsala University, Stockholm University and
+the Royal Institute of Technology, Sweden.
+check out http://www.gromacs.org for more information.
+
+GROMACS is free software; you can redistribute it and/or modify it
+under the terms of the GNU Lesser General Public License
+as published by the Free Software Foundation; either version 2.1
+of the License, or (at your option) any later version.
+
+GROMACS:      gmx mdrun, version 2019.1
+Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
+Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
+Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/NPT
+Command line:
+  gmx mdrun -deffnm npt2
+
+Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
+The current CPU can measure timings more accurately than the code in
+gmx mdrun was configured to use. This might affect your simulation
+speed as accurate timings are needed for load-balancing.
+Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
+Reading file npt2.tpr, VERSION 2019.1 (single precision)
+Changing nstlist from 20 to 100, rlist from 1.2 to 1.2
+
+
+Using 1 MPI thread
+Using 4 OpenMP threads
+
+starting mdrun 'BioSimSpace System'
+50 steps,      0.1 ps.
+
+Writing final coordinates.
+
+               Core t (s)   Wall t (s)        (%)
+       Time:        1.290        0.323      399.9
+                 (ns/day)    (hour/ns)
+Performance:       13.659        1.757
+
+GROMACS reminds you: "People are DNA's way of making more DNA." (Edward O. Wilson)
+
+Constant pressure equilibration complete.
+Starting production MD simulation...
+                      :-) GROMACS - gmx grompp, 2019.1 (-:
+
+                            GROMACS is written by:
+     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
+    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd
+ Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray
+  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang
+  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
+    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson
+  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund
+    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall
+    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov
+   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen
+ Christian Wennberg    Maarten Wolf
+                           and the project leaders:
+        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
+
+Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+Copyright (c) 2001-2018, The GROMACS development team at
+Uppsala University, Stockholm University and
+the Royal Institute of Technology, Sweden.
+check out http://www.gromacs.org for more information.
+
+GROMACS is free software; you can redistribute it and/or modify it
+under the terms of the GNU Lesser General Public License
+as published by the Free Software Foundation; either version 2.1
+of the License, or (at your option) any later version.
+
+GROMACS:      gmx grompp, version 2019.1
+Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
+Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
+Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/Production_MD
+Command line:
+  gmx grompp -f /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_2.mdp -c ../NPT/npt2.gro -p /tmp/tmphozbbmzv/job_working_directory/000/3/working/morph.top -t ../NPT/npt2.cpt -o md2.tpr
+
+
+NOTE 1 [file /tmp/tmphozbbmzv/job_working_directory/000/3/working/MDP/md_2.mdp]:
+  With PME there is a minor soft core effect present at the cut-off,
+  proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on
+  energy conservation, but usually other effects dominate. With a common
+  sigma value of 0.34 nm the fraction of the particle-particle potential at
+  the cut-off at lambda=0.5 is around 2.5e-04, while ewald-rtol is 1.0e-05.
+
+Setting the LD random seed to 551042888
+Generated 45 of the 45 non-bonded parameter combinations
+Generating 1-4 interactions: fudge = 0.5
+Generated 45 of the 45 1-4 parameter combinations
+Excluding 3 bonded neighbours molecule type 'Merged_Molecule'
+Excluding 3 bonded neighbours molecule type 'NA'
+Excluding 3 bonded neighbours molecule type 'CL'
+Excluding 3 bonded neighbours molecule type 'WAT'
+Removing all charge groups because cutoff-scheme=Verlet
+
+NOTE 2 [file morph.top, line 232]:
+  The bond in molecule-type Merged_Molecule between atoms 7 H and 13 H has
+  an estimated oscillational period of 8.0e-03 ps, which is less than 10
+  times the time step of 1.0e-03 ps.
+  Maybe you forgot to change the constraints mdp option.
+
+Number of degrees of freedom in T-Coupling group System is 12987.00
+Reading Coordinates, Velocities and Box size from old trajectory
+Will read whole trajectory
+
Last frame         -1 time    0.050
+Using frame at t = 0.05 ps
+Starting time for run is 0 ps
+Estimate for the relative computational load of the PME mesh part: 0.47
+
+There were 2 notes
+
+GROMACS reminds you: "Wedged as we are between two eternities of idleness, there is no excuse for being idle now" (Anthony Burgess)
+
+Analysing residue names:
+There are:     1      Other residues
+There are:    10        Ion residues
+There are:  2151      Water residues
+Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
+Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
+Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
+Calculated rlist for 1x1 atom pair-list as 0.812 nm, buffer size 0.012 nm
+Set rlist, assuming 4x4 atom pair-list, to 0.800 nm, buffer size 0.000 nm
+Note that mdrun will redetermine rlist based on the actual pair-list setup
+Calculating fourier grid dimensions for X Y Z
+Using a fourier grid of 42x42x42, spacing 0.096 0.096 0.096
+This run will generate roughly 1 Mb of data
+                      :-) GROMACS - gmx mdrun, 2019.1 (-:
+
+                            GROMACS is written by:
+     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
+    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd
+ Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray
+  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang
+  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
+    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson
+  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund
+    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall
+    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov
+   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen
+ Christian Wennberg    Maarten Wolf
+                           and the project leaders:
+        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
+
+Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+Copyright (c) 2001-2018, The GROMACS development team at
+Uppsala University, Stockholm University and
+the Royal Institute of Technology, Sweden.
+check out http://www.gromacs.org for more information.
+
+GROMACS is free software; you can redistribute it and/or modify it
+under the terms of the GNU Lesser General Public License
+as published by the Free Software Foundation; either version 2.1
+of the License, or (at your option) any later version.
+
+GROMACS:      gmx mdrun, version 2019.1
+Executable:   /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1/bin/gmx
+Data prefix:  /home/people/tsenapathi/miniconda3/envs/__gromacs@2019.1
+Working dir:  /tmp/tmphozbbmzv/job_working_directory/000/3/working/Lambda_2/Production_MD
+Command line:
+  gmx mdrun -deffnm md2
+
+Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
+The current CPU can measure timings more accurately than the code in
+gmx mdrun was configured to use. This might affect your simulation
+speed as accurate timings are needed for load-balancing.
+Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
+Reading file md2.tpr, VERSION 2019.1 (single precision)
+Changing nstlist from 10 to 50, rlist from 0.8 to 0.86
+
+
+Using 1 MPI thread
+Using 4 OpenMP threads
+
+starting mdrun 'BioSimSpace System'
+2000 steps,      2.0 ps.
+
+step 2: One or more water molecules can not be settled.
+Check for bad contacts and/or reduce the timestep if appropriate.
+Wrote pdb files with previous and current coordinates
+
+WARNING: Listed nonbonded interaction between particles 6 and 15
+at distance 47.750 which is larger than the table limit 1.860 nm.
+
+This is likely either a 1,4 interaction, or a listed interaction inside
+a smaller molecule you are decoupling during a free energy calculation.
+Since interactions at distances beyond the table cannot be computed,
+they are skipped until they are inside the table limit again. You will
+only see this message once, even if it occurs for several interactions.
+
+IMPORTANT: This should not happen in a stable simulation, so there is
+probably something wrong with your system. Only change the table-extension
+distance in the mdp file if you are really sure that is the reason.
+
+
+
+WARNING: Listed nonbonded interaction between particles 2 and 15
+at distance 47.627 which is larger than the table limit 1.860 nm.
+
+This is likely either a 1,4 interaction, or a listed interaction inside
+a smaller molecule you are decoupling during a free energy calculation.
+Since interactions at distances beyond the table cannot be computed,
+they are skipped until they are inside the table limit again. You will
+only see this message once, even if it occurs for several interactions.
+
+IMPORTANT: This should not happen in a stable simulation, so there is
+probably something wrong with your system. Only change the table-extension
+distance in the mdp file if you are really sure that is the reason.
+
+
+/scratch2/tsenapathi/Projects/BRIDGE/galaxy-tools-compchem/tools/free_energy/alchemical_run/gmx_fep.sh: line 104: 13890 Segmentation fault      gmx mdrun -deffnm md$LAMBDA
+Production MD complete.
+Ending. Job completed for lambda = 2
Binary file alchemical_run/test-data/TI_FEP_data_output.tar has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alchemical_run/test-data/morph.gro	Mon Nov 11 13:20:39 2019 -0500
@@ -0,0 +1,6484 @@
+GROningen MAchine for Chemical Simulation
+ 6481
+    1LIG      C    1   1.955   1.939   2.023
+    1LIG     C1    2   1.997   1.913   1.895
+    1LIG     C2    3   2.091   1.992   1.835
+    1LIG     C3    4   2.141   2.098   1.902
+    1LIG     C4    5   2.099   2.126   2.030
+    1LIG     C5    6   2.007   2.044   2.092
+    1LIG      H    7   1.881   1.875   2.069
+    1LIG     H1    8   1.955   1.829   1.841
+    1LIG     H2    9   2.124   1.970   1.734
+    1LIG     H3   10   2.215   2.162   1.854
+    1LIG     H4   11   2.140   2.211   2.084
+    1LIG     H5   12   1.975   2.064   2.193
+    1LIG      H   13   1.838   1.789   2.010
+    1LIG     H1   14   1.921   1.817   2.156
+    1LIG     H2   15   1.786   1.927   2.095
+    1LIG     H7   16   2.022   2.150   2.248
+    1LIG     H8   17   1.868   2.096   2.200
+    1LIG     H9   18   1.999   1.983   2.266
+    2NA      NA   19   0.461   1.266   1.727
+    3NA      NA   20   0.225   2.137   2.858
+    4NA      NA   21   1.400   3.831   0.426
+    5NA      NA   22   0.614   3.846   1.979
+    6NA      NA   23   2.064   2.147   3.360
+    7CL      CL   24   1.730   0.934   1.517
+    8CL      CL   25   0.594   0.745   2.514
+    9CL      CL   26   0.473   4.224   3.915
+   10CL      CL   27   2.721   1.374   0.016
+   11CL      CL   28   2.244   0.700   2.342
+   12WAT      O   29   0.230   0.628   0.113
+   12WAT     H1   30   0.137   0.626   0.150
+   12WAT     H2   31   0.231   0.589   0.021
+   13WAT      O   32   0.225   0.275   0.996
+   13WAT     H1   33   0.260   0.258   1.088
+   13WAT     H2   34   0.137   0.230   0.984
+   14WAT      O   35   0.019   0.368   0.647
+   14WAT     H1   36  -0.063   0.411   0.686
+   14WAT     H2   37  -0.009   0.295   0.584
+   15WAT      O   38   0.569   1.275   1.165
+   15WAT     H1   39   0.476   1.268   1.128
+   15WAT     H2   40   0.580   1.364   1.209
+   16WAT      O   41   1.555   1.511   0.703
+   16WAT     H1   42   1.498   1.495   0.784
+   16WAT     H2   43   1.496   1.521   0.623
+   17WAT      O   44   1.135   0.703   0.717
+   17WAT     H1   45   1.192   0.781   0.692
+   17WAT     H2   46   1.075   0.729   0.793
+   18WAT      O   47   1.755   0.607   0.231
+   18WAT     H1   48   1.743   0.594   0.132
+   18WAT     H2   49   1.725   0.526   0.280
+   19WAT      O   50   0.768   1.144   1.023
+   19WAT     H1   51   0.690   1.161   1.083
+   19WAT     H2   52   0.802   1.231   0.987
+   20WAT      O   53   0.850   0.798   1.823
+   20WAT     H1   54   0.846   0.874   1.888
+   20WAT     H2   55   0.872   0.834   1.732
+   21WAT      O   56   0.685   1.012   0.665
+   21WAT     H1   57   0.754   0.996   0.735
+   21WAT     H2   58   0.612   1.069   0.703
+   22WAT      O   59   0.686   1.161   1.803
+   22WAT     H1   60   0.746   1.240   1.817
+   22WAT     H2   61   0.600   1.192   1.762
+   23WAT      O   62   0.335   1.435   1.061
+   23WAT     H1   63   0.257   1.404   1.008
+   23WAT     H2   64   0.393   1.493   1.004
+   24WAT      O   65   1.460   1.505   1.339
+   24WAT     H1   66   1.484   1.599   1.365
+   24WAT     H2   67   1.444   1.451   1.421
+   25WAT      O   68   0.438   0.392   1.499
+   25WAT     H1   69   0.520   0.336   1.508
+   25WAT     H2   70   0.357   0.334   1.503
+   26WAT      O   71   1.603   0.447   0.737
+   26WAT     H1   72   1.529   0.493   0.687
+   26WAT     H2   73   1.654   0.515   0.790
+   27WAT      O   74   0.231   1.713   0.483
+   27WAT     H1   75   0.265   1.790   0.537
+   27WAT     H2   76   0.275   1.713   0.393
+   28WAT      O   77   1.127   1.341   1.690
+   28WAT     H1   78   1.174   1.341   1.778
+   28WAT     H2   79   1.079   1.254   1.679
+   29WAT      O   80   0.230   1.434   0.538
+   29WAT     H1   81   0.204   1.530   0.538
+   29WAT     H2   82   0.159   1.380   0.583
+   30WAT      O   83   0.240   1.091   0.886
+   30WAT     H1   84   0.254   1.007   0.938
+   30WAT     H2   85   0.185   1.155   0.941
+   31WAT      O   86   0.620   1.786   1.439
+   31WAT     H1   87   0.528   1.769   1.474
+   31WAT     H2   88   0.648   1.878   1.465
+   32WAT      O   89   0.606   0.964   0.123
+   32WAT     H1   90   0.613   1.048   0.069
+   32WAT     H2   91   0.652   0.977   0.211
+   33WAT      O   92   1.594   0.114   1.480
+   33WAT     H1   93   1.576   0.181   1.408
+   33WAT     H2   94   1.591   0.160   1.569
+   34WAT      O   95   0.122   0.643   0.563
+   34WAT     H1   96   0.077   0.555   0.580
+   34WAT     H2   97   0.121   0.697   0.647
+   35WAT      O   98   1.842   1.767   0.359
+   35WAT     H1   99   1.896   1.738   0.439
+   35WAT     H2  100   1.872   1.857   0.330
+   36WAT      O  101   0.027   1.596   0.117
+   36WAT     H1  102   0.008   1.500   0.138
+   36WAT     H2  103  -0.006   1.654   0.192
+   37WAT      O  104   1.689   0.922   0.612
+   37WAT     H1  105   1.784   0.893   0.620
+   37WAT     H2  106   1.681   0.987   0.537
+   38WAT      O  107   1.641   1.108   0.432
+   38WAT     H1  108   1.727   1.110   0.380
+   38WAT     H2  109   1.655   1.155   0.520
+   39WAT      O  110   0.113   0.737   1.597
+   39WAT     H1  111   0.201   0.724   1.642
+   39WAT     H2  112   0.100   0.834   1.575
+   40WAT      O  113   0.613   1.365   0.726
+   40WAT     H1  114   0.564   1.278   0.735
+   40WAT     H2  115   0.590   1.408   0.639
+   41WAT      O  116   1.293   1.228   1.423
+   41WAT     H1  117   1.330   1.155   1.365
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+  605WAT     H2 1810   0.548   3.351   0.868
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+  606WAT     H2 1813   0.906   2.631   1.235
+  607WAT      O 1814   0.040   2.406   1.114
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+  607WAT     H2 1816   0.053   2.421   1.212
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+  608WAT     H2 1819   0.131   2.453   1.681
+  609WAT      O 1820   1.369   2.812   1.660
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+  609WAT     H2 1822   1.379   2.792   1.563
+  610WAT      O 1823   0.815   2.434   0.325
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+  610WAT     H2 1825   0.721   2.468   0.317
+  611WAT      O 1826   1.657   2.466   1.206
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+  611WAT     H2 1828   1.739   2.430   1.162
+  612WAT      O 1829   0.252   3.426   1.744
+  612WAT     H1 1830   0.222   3.483   1.820
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+  615WAT     H1 1839   0.534   2.442   0.195
+  615WAT     H2 1840   0.378   2.393   0.198
+  616WAT      O 1841   0.159   2.999   1.466
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+  617WAT      O 1844   1.347   2.921   1.234
+  617WAT     H1 1845   1.371   2.858   1.160
+  617WAT     H2 1846   1.257   2.961   1.216
+  618WAT      O 1847   1.302   2.717   0.309
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+ 1964WAT     H2 5887   2.571   3.736   2.370
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+ 2076WAT      O 6221   3.955   3.575   0.483
+ 2076WAT     H1 6222   3.989   3.652   0.537
+ 2076WAT     H2 6223   3.999   3.575   0.393
+ 2077WAT      O 6224   3.954   3.296   0.538
+ 2077WAT     H1 6225   3.928   3.392   0.538
+ 2077WAT     H2 6226   3.883   3.242   0.583
+ 2078WAT      O 6227   3.846   2.505   0.563
+ 2078WAT     H1 6228   3.801   2.417   0.580
+ 2078WAT     H2 6229   3.845   2.559   0.647
+ 2079WAT      O 6230   3.751   3.458   0.117
+ 2079WAT     H1 6231   3.732   3.362   0.138
+ 2079WAT     H2 6232   3.718   3.516   0.192
+ 2080WAT      O 6233   3.837   2.599   1.597
+ 2080WAT     H1 6234   3.925   2.586   1.642
+ 2080WAT     H2 6235   3.824   2.696   1.575
+ 2081WAT      O 6236   3.800   2.673   0.789
+ 2081WAT     H1 6237   3.899   2.661   0.798
+ 2081WAT     H2 6238   3.776   2.768   0.810
+ 2082WAT      O 6239   3.854   3.683   1.571
+ 2082WAT     H1 6240   3.844   3.668   1.670
+ 2082WAT     H2 6241   3.768   3.719   1.535
+ 2083WAT      O 6242   3.926   2.147   1.498
+ 2083WAT     H1 6243   3.846   2.207   1.485
+ 2083WAT     H2 6244   3.916   2.098   1.584
+ 2084WAT      O 6245   4.021   1.897   0.171
+ 2084WAT     H1 6246   4.070   1.981   0.150
+ 2084WAT     H2 6247   4.083   1.832   0.216
+ 2085WAT      O 6248   3.802   2.418   1.386
+ 2085WAT     H1 6249   3.894   2.417   1.345
+ 2085WAT     H2 6250   3.796   2.492   1.453
+ 2086WAT      O 6251   4.251   2.118   0.328
+ 2086WAT     H1 6252   4.278   2.059   0.253
+ 2086WAT     H2 6253   4.251   2.213   0.297
+ 2087WAT      O 6254   3.788   3.426   1.331
+ 2087WAT     H1 6255   3.742   3.508   1.297
+ 2087WAT     H2 6256   3.886   3.445   1.340
+ 2088WAT      O 6257   4.091   2.962   0.501
+ 2088WAT     H1 6258   4.084   3.045   0.445
+ 2088WAT     H2 6259   4.095   2.882   0.441
+ 2089WAT      O 6260   4.031   2.075   1.231
+ 2089WAT     H1 6261   4.008   2.112   1.321
+ 2089WAT     H2 6262   4.001   1.980   1.225
+ 2090WAT      O 6263   3.761   3.172   1.282
+ 2090WAT     H1 6264   3.814   3.123   1.350
+ 2090WAT     H2 6265   3.783   3.270   1.287
+ 2091WAT      O 6266   4.031   1.925   0.618
+ 2091WAT     H1 6267   4.020   2.019   0.651
+ 2091WAT     H2 6268   4.026   1.862   0.695
+ 2092WAT      O 6269   3.732   3.188   0.200
+ 2092WAT     H1 6270   3.639   3.209   0.169
+ 2092WAT     H2 6271   3.742   3.089   0.213
+ 2093WAT      O 6272   3.812   3.663   0.927
+ 2093WAT     H1 6273   3.770   3.577   0.900
+ 2093WAT     H2 6274   3.906   3.666   0.893
+ 2094WAT      O 6275   4.228   3.430   0.910
+ 2094WAT     H1 6276   4.294   3.504   0.919
+ 2094WAT     H2 6277   4.272   3.351   0.868
+ 2095WAT      O 6278   3.764   2.406   1.114
+ 2095WAT     H1 6279   3.849   2.373   1.073
+ 2095WAT     H2 6280   3.777   2.421   1.212
+ 2096WAT      O 6281   3.913   2.382   1.722
+ 2096WAT     H1 6282   3.972   2.342   1.652
+ 2096WAT     H2 6283   3.855   2.453   1.681
+ 2097WAT      O 6284   3.976   3.426   1.744
+ 2097WAT     H1 6285   3.946   3.483   1.820
+ 2097WAT     H2 6286   3.969   3.329   1.770
+ 2098WAT      O 6287   3.883   2.999   1.466
+ 2098WAT     H1 6288   3.905   2.938   1.542
+ 2098WAT     H2 6289   3.893   2.950   1.380
+ 2099WAT      O 6290   3.807   3.120   1.022
+ 2099WAT     H1 6291   3.802   3.119   1.122
+ 2099WAT     H2 6292   3.724   3.079   0.984
+ 2100WAT      O 6293   3.854   3.656   1.851
+ 2100WAT     H1 6294   3.813   3.582   1.904
+ 2100WAT     H2 6295   3.918   3.707   1.909
+ 2101WAT      O 6296   3.799   2.207   0.033
+ 2101WAT     H1 6297   3.707   2.179   0.004
+ 2101WAT     H2 6298   3.830   2.284  -0.023
+ 2102WAT      O 6299   3.796   2.028   0.318
+ 2102WAT     H1 6300   3.779   2.111   0.264
+ 2102WAT     H2 6301   3.886   1.991   0.296
+ 2103WAT      O 6302   3.803   3.102   0.653
+ 2103WAT     H1 6303   3.802   3.055   0.741
+ 2103WAT     H2 6304   3.885   3.074   0.602
+ 2104WAT      O 6305   3.763   2.939   0.300
+ 2104WAT     H1 6306   3.862   2.928   0.291
+ 2104WAT     H2 6307   3.723   2.853   0.332
+ 2105WAT      O 6308   3.954   2.490   1.975
+ 2105WAT     H1 6309   3.861   2.488   2.012
+ 2105WAT     H2 6310   3.955   2.451   1.883
+ 2106WAT      O 6311   3.949   2.137   2.858
+ 2106WAT     H1 6312   3.984   2.120   2.950
+ 2106WAT     H2 6313   3.861   2.092   2.846
+ 2107WAT      O 6314   3.743   2.230   2.509
+ 2107WAT     H1 6315   3.661   2.273   2.548
+ 2107WAT     H2 6316   3.715   2.157   2.446
+ 2108WAT      O 6317   4.059   3.297   2.923
+ 2108WAT     H1 6318   3.981   3.266   2.870
+ 2108WAT     H2 6319   4.117   3.355   2.866
+ 2109WAT      O 6320   3.955   3.575   2.345
+ 2109WAT     H1 6321   3.989   3.652   2.399
+ 2109WAT     H2 6322   3.999   3.575   2.255
+ 2110WAT      O 6323   3.954   3.296   2.400
+ 2110WAT     H1 6324   3.928   3.392   2.400
+ 2110WAT     H2 6325   3.883   3.242   2.445
+ 2111WAT      O 6326   3.846   2.505   2.425
+ 2111WAT     H1 6327   3.801   2.417   2.442
+ 2111WAT     H2 6328   3.845   2.559   2.509
+ 2112WAT      O 6329   3.751   3.458   1.979
+ 2112WAT     H1 6330   3.732   3.362   2.000
+ 2112WAT     H2 6331   3.718   3.516   2.054
+ 2113WAT      O 6332   3.837   2.599   3.459
+ 2113WAT     H1 6333   3.925   2.586   3.504
+ 2113WAT     H2 6334   3.824   2.696   3.437
+ 2114WAT      O 6335   3.800   2.673   2.651
+ 2114WAT     H1 6336   3.899   2.661   2.660
+ 2114WAT     H2 6337   3.776   2.768   2.672
+ 2115WAT      O 6338   3.854   3.683   3.433
+ 2115WAT     H1 6339   3.844   3.668   3.532
+ 2115WAT     H2 6340   3.768   3.719   3.397
+ 2116WAT      O 6341   3.926   2.147   3.360
+ 2116WAT     H1 6342   3.846   2.207   3.347
+ 2116WAT     H2 6343   3.916   2.098   3.446
+ 2117WAT      O 6344   4.021   1.897   2.033
+ 2117WAT     H1 6345   4.070   1.981   2.012
+ 2117WAT     H2 6346   4.083   1.832   2.078
+ 2118WAT      O 6347   3.802   2.418   3.248
+ 2118WAT     H1 6348   3.894   2.417   3.207
+ 2118WAT     H2 6349   3.796   2.492   3.315
+ 2119WAT      O 6350   4.251   2.118   2.190
+ 2119WAT     H1 6351   4.278   2.059   2.115
+ 2119WAT     H2 6352   4.251   2.213   2.159
+ 2120WAT      O 6353   3.788   3.426   3.193
+ 2120WAT     H1 6354   3.742   3.508   3.159
+ 2120WAT     H2 6355   3.886   3.445   3.202
+ 2121WAT      O 6356   4.091   2.962   2.363
+ 2121WAT     H1 6357   4.084   3.045   2.307
+ 2121WAT     H2 6358   4.095   2.882   2.303
+ 2122WAT      O 6359   4.031   2.075   3.093
+ 2122WAT     H1 6360   4.008   2.112   3.183
+ 2122WAT     H2 6361   4.001   1.980   3.087
+ 2123WAT      O 6362   3.761   3.172   3.144
+ 2123WAT     H1 6363   3.814   3.123   3.212
+ 2123WAT     H2 6364   3.783   3.270   3.149
+ 2124WAT      O 6365   4.031   1.925   2.480
+ 2124WAT     H1 6366   4.020   2.019   2.513
+ 2124WAT     H2 6367   4.026   1.862   2.557
+ 2125WAT      O 6368   3.732   3.188   2.062
+ 2125WAT     H1 6369   3.639   3.209   2.031
+ 2125WAT     H2 6370   3.742   3.089   2.075
+ 2126WAT      O 6371   3.812   3.663   2.789
+ 2126WAT     H1 6372   3.770   3.577   2.762
+ 2126WAT     H2 6373   3.906   3.666   2.755
+ 2127WAT      O 6374   4.228   3.430   2.772
+ 2127WAT     H1 6375   4.294   3.504   2.781
+ 2127WAT     H2 6376   4.272   3.351   2.730
+ 2128WAT      O 6377   3.764   2.406   2.976
+ 2128WAT     H1 6378   3.849   2.373   2.935
+ 2128WAT     H2 6379   3.777   2.421   3.074
+ 2129WAT      O 6380   3.913   2.382   3.584
+ 2129WAT     H1 6381   3.972   2.342   3.514
+ 2129WAT     H2 6382   3.855   2.453   3.543
+ 2130WAT      O 6383   3.976   3.426   3.606
+ 2130WAT     H1 6384   3.946   3.483   3.682
+ 2130WAT     H2 6385   3.969   3.329   3.632
+ 2131WAT      O 6386   3.883   2.999   3.328
+ 2131WAT     H1 6387   3.905   2.938   3.404
+ 2131WAT     H2 6388   3.893   2.950   3.242
+ 2132WAT      O 6389   3.807   3.120   2.884
+ 2132WAT     H1 6390   3.802   3.119   2.984
+ 2132WAT     H2 6391   3.724   3.079   2.846
+ 2133WAT      O 6392   3.854   3.656   3.713
+ 2133WAT     H1 6393   3.813   3.582   3.766
+ 2133WAT     H2 6394   3.918   3.707   3.771
+ 2134WAT      O 6395   3.799   2.207   1.895
+ 2134WAT     H1 6396   3.707   2.179   1.866
+ 2134WAT     H2 6397   3.830   2.284   1.839
+ 2135WAT      O 6398   3.796   2.028   2.180
+ 2135WAT     H1 6399   3.779   2.111   2.126
+ 2135WAT     H2 6400   3.886   1.991   2.158
+ 2136WAT      O 6401   3.803   3.102   2.515
+ 2136WAT     H1 6402   3.802   3.055   2.603
+ 2136WAT     H2 6403   3.885   3.074   2.464
+ 2137WAT      O 6404   3.763   2.939   2.162
+ 2137WAT     H1 6405   3.862   2.928   2.153
+ 2137WAT     H2 6406   3.723   2.853   2.194
+ 2138WAT      O 6407   3.954   2.490   3.837
+ 2138WAT     H1 6408   3.861   2.488   3.874
+ 2138WAT     H2 6409   3.955   2.451   3.745
+ 2139WAT      O 6410   3.751   3.458   3.841
+ 2139WAT     H1 6411   3.732   3.362   3.862
+ 2139WAT     H2 6412   3.718   3.516   3.916
+ 2140WAT      O 6413   4.021   1.897   3.895
+ 2140WAT     H1 6414   4.070   1.981   3.874
+ 2140WAT     H2 6415   4.083   1.832   3.940
+ 2141WAT      O 6416   4.251   2.118   4.052
+ 2141WAT     H1 6417   4.278   2.059   3.977
+ 2141WAT     H2 6418   4.251   2.213   4.021
+ 2142WAT      O 6419   3.732   3.188   3.924
+ 2142WAT     H1 6420   3.639   3.209   3.893
+ 2142WAT     H2 6421   3.742   3.089   3.937
+ 2143WAT      O 6422   3.799   2.207   3.757
+ 2143WAT     H1 6423   3.707   2.179   3.728
+ 2143WAT     H2 6424   3.830   2.284   3.701
+ 2144WAT      O 6425   3.763   2.939   4.024
+ 2144WAT     H1 6426   3.862   2.928   4.015
+ 2144WAT     H2 6427   3.723   2.853   4.056
+ 2145WAT      O 6428   3.949   3.999   0.996
+ 2145WAT     H1 6429   3.984   3.982   1.088
+ 2145WAT     H2 6430   3.861   3.954   0.984
+ 2146WAT      O 6431   3.743   4.092   0.647
+ 2146WAT     H1 6432   3.661   4.135   0.686
+ 2146WAT     H2 6433   3.715   4.019   0.584
+ 2147WAT      O 6434   3.926   4.009   1.498
+ 2147WAT     H1 6435   3.846   4.069   1.485
+ 2147WAT     H2 6436   3.916   3.960   1.584
+ 2148WAT      O 6437   4.021   3.759   0.171
+ 2148WAT     H1 6438   4.070   3.843   0.150
+ 2148WAT     H2 6439   4.083   3.694   0.216
+ 2149WAT      O 6440   4.031   3.937   1.231
+ 2149WAT     H1 6441   4.008   3.974   1.321
+ 2149WAT     H2 6442   4.001   3.842   1.225
+ 2150WAT      O 6443   4.031   3.787   0.618
+ 2150WAT     H1 6444   4.020   3.881   0.651
+ 2150WAT     H2 6445   4.026   3.724   0.695
+ 2151WAT      O 6446   3.799   4.069   0.033
+ 2151WAT     H1 6447   3.707   4.041   0.004
+ 2151WAT     H2 6448   3.830   4.146  -0.023
+ 2152WAT      O 6449   3.796   3.890   0.318
+ 2152WAT     H1 6450   3.779   3.973   0.264
+ 2152WAT     H2 6451   3.886   3.853   0.296
+ 2153WAT      O 6452   3.949   3.999   2.858
+ 2153WAT     H1 6453   3.984   3.982   2.950
+ 2153WAT     H2 6454   3.861   3.954   2.846
+ 2154WAT      O 6455   3.743   4.092   2.509
+ 2154WAT     H1 6456   3.661   4.135   2.548
+ 2154WAT     H2 6457   3.715   4.019   2.446
+ 2155WAT      O 6458   3.926   4.009   3.360
+ 2155WAT     H1 6459   3.846   4.069   3.347
+ 2155WAT     H2 6460   3.916   3.960   3.446
+ 2156WAT      O 6461   4.021   3.759   2.033
+ 2156WAT     H1 6462   4.070   3.843   2.012
+ 2156WAT     H2 6463   4.083   3.694   2.078
+ 2157WAT      O 6464   4.031   3.937   3.093
+ 2157WAT     H1 6465   4.008   3.974   3.183
+ 2157WAT     H2 6466   4.001   3.842   3.087
+ 2158WAT      O 6467   4.031   3.787   2.480
+ 2158WAT     H1 6468   4.020   3.881   2.513
+ 2158WAT     H2 6469   4.026   3.724   2.557
+ 2159WAT      O 6470   3.799   4.069   1.895
+ 2159WAT     H1 6471   3.707   4.041   1.866
+ 2159WAT     H2 6472   3.830   4.146   1.839
+ 2160WAT      O 6473   3.796   3.890   2.180
+ 2160WAT     H1 6474   3.779   3.973   2.126
+ 2160WAT     H2 6475   3.886   3.853   2.158
+ 2161WAT      O 6476   4.021   3.759   3.895
+ 2161WAT     H1 6477   4.070   3.843   3.874
+ 2161WAT     H2 6478   4.083   3.694   3.940
+ 2162WAT      O 6479   3.799   4.069   3.757
+ 2162WAT     H1 6480   3.707   4.041   3.728
+ 2162WAT     H2 6481   3.830   4.146   3.701
+   4.00000   4.00000   4.00000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alchemical_run/test-data/morph.top	Mon Nov 11 13:20:39 2019 -0500
@@ -0,0 +1,232 @@
+; Gromacs Topology File written by Sire
+; File written 05/01/19  13:21:14
+[ defaults ]
+; nbfunc      comb-rule       gen-pairs      fudgeLJ     fudgeQQ
+  1           2               yes            0.5         0.833333
+
+[ atomtypes ]
+; name      at.num        mass      charge   ptype       sigma     epsilon
+   Cl-          17   35.453000    0.000000       A    0.447766    0.148913
+    HW           1    1.007940    0.000000       A    0.000000    0.000000
+   Na+          11   22.989770    0.000000       A    0.243928    0.365846
+    OW           8   15.999400    0.000000       A    0.315075    0.635968
+    c3           6   12.010700    0.000000       A    0.339771    0.451035
+    ca           6   12.010700    0.000000       A    0.331521    0.413379
+    ha           1    1.007940    0.000000       A    0.262548    0.067362
+    hc           1    1.007940    0.000000       A    0.260018    0.087027
+ hc_du           0    0.000000    0.000000       A    0.000000    0.000000
+
+[ moleculetype ]
+; name  nrexcl
+CL  3
+
+[ atoms ]
+;   nr   type  resnr residue  atom   cgnr     charge         mass
+     1    Cl-      1      CL    CL      1  -1.000000    35.450000
+
+
+[ moleculetype ]
+; name  nrexcl
+Merged_Molecule  3
+
+[ atoms ]
+;   nr   type0  resnr residue  atom   cgnr    charge0        mass0   type1    charge1        mass1
+     1      ca      1     LIG     C      1  -0.130000    12.010000      ca  -0.075744    12.010000
+     2      ca      1     LIG    C1      2  -0.130000    12.010000      ca  -0.129444    12.010000
+     3      ca      1     LIG    C2      3  -0.130000    12.010000      ca  -0.131444    12.010000
+     4      ca      1     LIG    C3      4  -0.130000    12.010000      ca  -0.131444    12.010000
+     5      ca      1     LIG    C4      5  -0.130000    12.010000      ca  -0.129444    12.010000
+     6      ca      1     LIG    C5      6  -0.130000    12.010000      ca  -0.075744    12.010000
+     7      ha      1     LIG     H      7   0.130000     1.008000      c3  -0.053744    12.010000
+     8      ha      1     LIG    H1      8   0.130000     1.008000      ha   0.129056     1.008000
+     9      ha      1     LIG    H2      9   0.130000     1.008000      ha   0.130056     1.008000
+    10      ha      1     LIG    H3     10   0.130000     1.008000      ha   0.130056     1.008000
+    11      ha      1     LIG    H4     11   0.130000     1.008000      ha   0.129056     1.008000
+    12      ha      1     LIG    H5     12   0.130000     1.008000      c3  -0.053744    12.010000
+    13   hc_du      1     LIG     H     13   0.000000     1.008000      hc   0.043756     1.008000
+    14   hc_du      1     LIG    H1     14   0.000000     1.008000      hc   0.043756     1.008000
+    15   hc_du      1     LIG    H2     15   0.000000     1.008000      hc   0.043756     1.008000
+    16   hc_du      1     LIG    H7     16   0.000000     1.008000      hc   0.043756     1.008000
+    17   hc_du      1     LIG    H8     17   0.000000     1.008000      hc   0.043756     1.008000
+    18   hc_du      1     LIG    H9     18   0.000000     1.008000      hc   0.043756     1.008000
+
+[ bonds ]
+;   ai     aj  funct  parameters
+     1      2      1  0.1398  316812  0.1398  316812
+     1      6      1  0.1398  316812  0.1398  316812
+     1      7      1  0.1086  331122  0.1516  209451
+     2      3      1  0.1398  316812  0.1398  316812
+     2      8      1  0.1086  331122  0.1086  331122
+     3      4      1  0.1398  316812  0.1398  316812
+     3      9      1  0.1086  331122  0.1086  331122
+     4      5      1  0.1398  316812  0.1398  316812
+     4     10      1  0.1086  331122  0.1086  331122
+     5      6      1  0.1398  316812  0.1398  316812
+     5     11      1  0.1086  331122  0.1086  331122
+     6     12      1  0.1086  331122  0.1516  209451
+     7     13      1  0.1097  314553  0.1097  314553
+     7     14      1  0.1097  314553  0.1097  314553
+     7     15      1  0.1097  314553  0.1097  314553
+    12     16      1  0.1097  314553  0.1097  314553
+    12     17      1  0.1097  314553  0.1097  314553
+    12     18      1  0.1097  314553  0.1097  314553
+
+[ pairs ]
+;   ai     aj funct
+     1      4     1
+     1      9     1
+     1     11     1
+     1     16     1
+     1     17     1
+     1     18     1
+     2      5     1
+     2     10     1
+     2     12     1
+     2     13     1
+     2     14     1
+     2     15     1
+     3      6     1
+     3      7     1
+     3     11     1
+     4      8     1
+     4     12     1
+     5      7     1
+     5      9     1
+     5     16     1
+     5     17     1
+     5     18     1
+     6      8     1
+     6     10     1
+     6     13     1
+     6     14     1
+     6     15     1
+     7      8     1
+     7     12     1
+     8      9     1
+     9     10     1
+    10     11     1
+    11     12     1
+
+[ angles ]
+;   ai     aj     ak   funct   parameters
+     1      2      3       1   120.02  575.718  120.02  575.718
+     1      2      8       1   119.88  407.522  119.88  407.522
+     1      6      5       1   120.02  575.718  120.02  575.718
+     1      6     12       1   119.88  407.522  120.77  548.941
+     1      7     13       1   110.47  395.806  110.47  395.806
+     1      7     14       1   110.47  395.806  110.47  395.806
+     1      7     15       1   110.47  395.806  110.47  395.806
+     2      1      6       1   120.02  575.718  120.02  575.718
+     2      1      7       1   119.88  407.522  120.77  548.941
+     2      3      4       1   120.02  575.718  120.02  575.718
+     2      3      9       1   119.88  407.522  119.88  407.522
+     3      2      8       1   119.88  407.522  119.88  407.522
+     3      4      5       1   120.02  575.718  120.02  575.718
+     3      4     10       1   119.88  407.522  119.88  407.522
+     4      3      9       1   119.88  407.522  119.88  407.522
+     4      5      6       1   120.02  575.718  120.02  575.718
+     4      5     11       1   119.88  407.522  119.88  407.522
+     5      4     10       1   119.88  407.522  119.88  407.522
+     5      6     12       1   119.88  407.522  120.77  548.941
+     6      1      7       1   119.88  407.522  120.77  548.941
+     6      5     11       1   119.88  407.522  119.88  407.522
+     6     12     16       1   110.47  395.806  110.47  395.806
+     6     12     17       1   110.47  395.806  110.47  395.806
+     6     12     18       1   110.47  395.806  110.47  395.806
+    13      7     14       1   107.58  326.352  107.58  326.352
+    13      7     15       1   107.58  326.352  107.58  326.352
+    14      7     15       1   107.58  326.352  107.58  326.352
+    16     12     17       1   107.58  326.352  107.58  326.352
+    16     12     18       1   107.58  326.352  107.58  326.352
+    17     12     18       1   107.58  326.352  107.58  326.352
+
+[ dihedrals ]
+;   ai     aj     ak     al  funct  parameters
+     1      2      3      4      1  180  15.167  2  180  15.167  2
+     1      2      3      9      1  180  15.167  2  180  15.167  2
+     1      3      2      8      4  180  4.6024  2  180  4.6024  2
+     1      5      6     12      4  180  4.6024  2  0  0  2
+     1      6      5      4      1  180  15.167  2  180  15.167  2
+     1      6      5     11      1  180  15.167  2  180  15.167  2
+     1      6     12     16      1  0  0  0  0  0  0
+     1      6     12     17      1  0  0  0  0  0  0
+     1      6     12     18      1  0  0  0  0  0  0
+     2      1      6      5      1  180  15.167  2  180  15.167  2
+     2      1      6     12      1  180  15.167  2  180  15.167  2
+     2      1      7     13      1  0  0  0  0  0  0
+     2      1      7     14      1  0  0  0  0  0  0
+     2      1      7     15      1  0  0  0  0  0  0
+     2      3      4      5      1  180  15.167  2  180  15.167  2
+     2      3      4     10      1  180  15.167  2  180  15.167  2
+     2      4      3      9      4  180  4.6024  2  180  4.6024  2
+     2      6      1      7      4  180  4.6024  2  180  4.6024  2
+     3      2      1      6      1  180  15.167  2  180  15.167  2
+     3      2      1      7      1  180  15.167  2  180  15.167  2
+     3      4      5      6      1  180  15.167  2  180  15.167  2
+     3      4      5     11      1  180  15.167  2  180  15.167  2
+     3      5      4     10      4  180  4.6024  2  180  4.6024  2
+     4      3      2      8      1  180  15.167  2  180  15.167  2
+     4      5      6     12      1  180  15.167  2  180  15.167  2
+     4      6      5     11      4  180  4.6024  2  180  4.6024  2
+     5      4      3      9      1  180  15.167  2  180  15.167  2
+     5      6      1      7      1  180  15.167  2  180  15.167  2
+     5      6      1     12      4  0  0  2  180  4.6024  2
+     5      6     12     16      1  0  0  0  0  0  0
+     5      6     12     17      1  0  0  0  0  0  0
+     5      6     12     18      1  0  0  0  0  0  0
+     6      1      2      8      1  180  15.167  2  180  15.167  2
+     6      1      7     13      1  0  0  0  0  0  0
+     6      1      7     14      1  0  0  0  0  0  0
+     6      1      7     15      1  0  0  0  0  0  0
+     6      5      4     10      1  180  15.167  2  180  15.167  2
+     7      1      2      8      1  180  15.167  2  180  15.167  2
+     7      1      6     12      1  180  15.167  2  180  15.167  2
+     8      2      3      9      1  180  15.167  2  180  15.167  2
+     9      3      4     10      1  180  15.167  2  180  15.167  2
+    10      4      5     11      1  180  15.167  2  180  15.167  2
+    11      5      6     12      1  180  15.167  2  180  15.167  2
+
+
+[ moleculetype ]
+; name  nrexcl
+NA  3
+
+[ atoms ]
+;   nr   type  resnr residue  atom   cgnr     charge         mass
+     1    Na+      1      NA    NA      1   1.000000    22.990000
+
+
+[ moleculetype ]
+; name  nrexcl
+WAT  3
+
+[ atoms ]
+;   nr   type  resnr residue  atom   cgnr     charge         mass
+     1     OW      1     WAT     O      1  -0.834000    16.000000
+     2     HW      1     WAT    H1      2   0.417000     1.008000
+     3     HW      1     WAT    H2      3   0.417000     1.008000
+
+#ifdef FLEXIBLE
+#else
+
+[ settles ]
+; OW    funct   doh dhh
+1       1       0.09572 0.15136
+
+[ exclusions ]
+1   2   3
+2   1   3
+3   1   2
+
+#endif
+
+[ system ]
+BioSimSpace System
+
+[ molecules ]
+;molecule name    nr.
+Merged_Molecule      1
+            NA      5
+            CL      5
+           WAT   2151
+