Mercurial > repos > chemteam > gmx_sim
diff sim.xml @ 0:1a5960636405 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
| author | chemteam |
|---|---|
| date | Mon, 07 Oct 2019 12:48:44 -0400 |
| parents | |
| children | ec3f665cca3e |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sim.xml Mon Oct 07 12:48:44 2019 -0400 @@ -0,0 +1,258 @@ +<tool id="gmx_sim" name="GROMACS simulation" version="@VERSION@"> + <description>for system equilibration or data collection</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + #if $mdp.mdpfile == "custom": + ln -s '$mdp.mdp_input' ./md.mdp && + #end if + #if $mdp.mdpfile == "default": + ln -s '$md' ./md.mdp && + #end if + + ln -s '$gro_input' ./inp.gro && + ln -s '$top_input' ./top_input.top && + + #if $posres.posres_bool == "true": + ln -s '$posres.itp_inp' ./posres.itp && + #end if + + #if $cpt_inp.cpt_bool == "yes": + ln -s '$cpt_inp.cpt_in' ./inp.cpt && + #end if + + gmx grompp + -f ./md.mdp + -c ./inp.gro + #if $cpt_inp.cpt_bool == "yes": + -t ./inp.cpt + #end if + #if $posres.posres_bool == "true": + -r ./inp.gro + #end if + -p ./top_input.top + -o outp.tpr &>> verbose.txt && + + + gmx mdrun -deffnm outp &>> verbose.txt + + #if $str == 'pdb' or $str == 'both' + && gmx editconf -f outp.gro -o outp.pdb &>> verbose.txt + #end if + + && cat md.mdp &>> verbose.txt + + ]]></command> + <configfiles> + <!-- .mdp file for the gromacs simulation --> + <configfile name="md"> + #if $mdp.mdpfile == 'default': + title = OPLS Lysozyme MD simulation + ; Run parameters + integrator = $mdp.integrator ; leap-frog integrator + nsteps = $mdp.md_steps ; 2 * 500000 = 1000 ps (1 ns) + dt = $mdp.step_length ; 2 fs + ; Output control + nstxout = $mdp.write_freq ; save coordinates every 10.0 ps + nstvout = $mdp.write_freq ; save velocities every 10.0 ps + nstenergy = $mdp.write_freq ; save energies every 10.0 ps + nstlog = $mdp.write_freq ; update log file every 10.0 ps + nstxout-compressed = $mdp.write_freq ; save compressed coordinates every 10.0 ps + ; nstxout-compressed replaces nstxtcout + compressed-x-grps = System ; group(s) to write to the compressed trajectory file + ; Bond parameters + continuation = $cpt_inp.cpt_bool ; Restarting after NPT + constraint_algorithm = lincs ; holonomic constraints + constraints = $mdp.constraints ; all bonds (even heavy atom-H bonds) constrained + lincs_iter = 1 ; accuracy of LINCS + lincs_order = 4 ; also related to accuracy + ; Neighborsearching + cutoff-scheme = $mdp.cutoffscheme + ns_type = grid ; search neighboring grid cells + nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme + rcoulomb = $mdp.rcoulomb ; Short-range electrostatic cut-off + rlist = $mdp.rlist ; Cut-off distance for the short-range neighbor list. + rvdw = $mdp.rvdw ; Short-range Van der Waals cut-off + ; Electrostatics + coulombtype = $mdp.coulombtype ; method for electrostatics calculations e.g. PME + pme_order = 4 ; cubic interpolation + fourierspacing = 0.16 ; grid spacing for FFT + ; Temperature coupling is on + tcoupl = V-rescale ; modified Berendsen thermostat + tc-grps = Protein Non-Protein ; two coupling groups - more accurate + tau_t = 0.1 0.1 ; time constant, in ps + ref_t = $mdp.temperature $mdp.temperature ; reference temperature, one for each group, in K + ; Periodic boundary conditions + pbc = xyz ; 3-D PBC + ; Dispersion correction + DispCorr = EnerPres ; account for cut-off vdW scheme + ; Velocity generation + gen_vel = no ; Velocity generation is off + #end if + #if $posres.posres_bool == "true": + define = -DPOSRES ; position restrain the protein + refcoord_scaling = com + #end if + #if $ensemble == "nvt": + pcoupl = no ; no pressure coupling in NVT + #else: + ; Pressure coupling is on + pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT + pcoupltype = isotropic ; uniform scaling of box vectors + tau_p = 2.0 ; time constant, in ps + ref_p = 1.0 ; reference pressure, in bar + compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 + #end if + + </configfile> + + </configfiles> + <inputs> + <param argument="gro_input" type="data" format='gro' label="GRO structure file"/> + <param argument="top_input" type="data" format='top' label="Topology (TOP) file"/> + <conditional name="cpt_inp"> + <param name="cpt_bool" type="select" label="Use a checkpoint (CPT) file" help="CPT file from a previous MD run"> + <option value="yes">Continue simulation from a CPT file</option> + <option value="no" selected="true">No CPT input</option> + </param> + <when value="yes"> + <param argument="cpt_in" type="data" format='cpt' label="Checkpoint file"/> + </when> + <when value="no"/> + </conditional> + <param name="cpt_out" type="select" label="Produce a checkpoint (CPT) file" help="Produce CPT file for a subsequent MD run"> + <option value="true">Produce CPT output</option> + <option value="false" selected="true">No CPT output</option> + </param> + + <conditional name="posres"> + <param name="posres_bool" type="select" label="Apply position restraints" help="Used e.g. for equilibration of solvent around a protein" value="false"> + <option value="true">Apply position restraints</option> + <option value="false" selected="true">No position restraints</option> + </param> + <when value="true"> + <param argument="itp_inp" type="data" format='itp' label="Position restraint (ITP) file"/> + </when> + <when value="false"/> + </conditional> + + <param name="ensemble" label="Ensemble" type="select" help="NVT ensemble (constant number of particles, volume and temperature) or NPT ensemble (constant number of particles, pressure and temperature)"> + <option value="nvt">Isothermal-isochoric ensemble (NVT)</option> + <option value="npt">Isothermal-isobaric ensemble (NPT)</option> + </param> + + <expand macro="md_inputs"/> + </inputs> + <outputs> + <data name="output1" format="gro" from_work_dir="outp.gro"> + <filter>str == 'gro' or str == 'both'</filter> + </data> + <data name="output2" format="pdb" from_work_dir="outp.pdb"> + <filter>str == 'pdb' or str == 'both'</filter> + </data> + <data name="output3" format="trr" from_work_dir="outp.trr"> + <filter>traj == 'trr' or traj == 'both'</filter> + </data> + <data name="output4" format="xtc" from_work_dir="outp.xtc"> + <filter>traj == 'xtc' or traj == 'both'</filter> + </data> + <data name="output5" format="cpt" from_work_dir="outp.cpt"> + <filter>cpt_out</filter> + </data> + + <data name="report" format="txt" from_work_dir="verbose.txt"> + <filter>capture_log</filter> + </data> + </outputs> + + <tests> + <test> + <param name="gro_input" value="npt.gro" /> + <param name="top_input" value="topol_solv.top" /> + <param name="cpt_bool" value="yes" /> + <param name="cpt_in" value="npt.cpt" /> + <param name="mdpfile" value="custom" /> + <param name="mdp_input" value="md.mdp" /> + <param name="traj" value="trr"/> + <param name="str" value="gro"/> + <param name="ensemble" value="npt" /> + <param name="posres_bool" value="false" /> + <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/> + <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/> + </test> + + <test> + <param name="gro_input" value="npt.gro" /> + <param name="top_input" value="topol_solv.top" /> + <param name="cpt_bool" value="yes" /> + <param name="cpt_in" value="npt.cpt" /> + <param name="traj" value="trr"/> + <param name="str" value="both"/> + <expand macro="test_params"/> + <param name="ensemble" value="npt" /> + <param name="posres_bool" value="false" /> + <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/> + <output name="output2" file="md_0_1.pdb" ftype="pdb" compare="sim_size"/> + <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/> + </test> + + <test> + <param name="gro_input" value="em.gro" /> + <param name="top_input" value="topol_solv.top" /> + <param name="posres_bool" value="true" /> + <param name="itp_inp" value="posres.itp" /> + <param name="cpt_bool" value="no" /> + <param name="cpt_out" value="true" /> + <param name="traj" value="xtc"/> + <param name="str" value="pdb"/> + <param name="ensemble" value="nvt" /> + <expand macro="test_params"/> + + <output name="output2" file="nvt.pdb" ftype="pdb" compare="sim_size"/> + <output name="output4" file="nvt.xtc" ftype="xtc" compare="sim_size"/> + <output name="output5" file="nvt.cpt" ftype="cpt" compare="sim_size"/> + + </test> + </tests> + + <help><![CDATA[ + +.. class:: infomark + +**What it does** + +This tool performs a molecular dynamics simulation with GROMACS. + +_____ + +.. class:: infomark + +**Input** + + - GRO structure file. + - Topology (TOP) file. + +A variety of other options can also be specified: + - MDP parameter file to take advantage of all GROMACS features. Otherwise, choose parameters through the Galaxy interface. See the `manual`_ for more information on the options. + - Accepting and producing checkpoint (CPT) input/output files, which allows sequential MD simulations, e.g. when performing NVT and NPT equilibration followed by a production simulation. + - Position restraint (ITP) file, useful for equilibrating solvent around a protein. + - Choice of ensemble: NVT or NPT. + - Whether to return trajectory (XTC or TRR) and/or structure (GRO or PDB) files. + +.. _`manual`: http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html + +_____ + + +.. class:: infomark + +**Output** + + - Structure and/or trajectory files as specified in the input. + + ]]></help> + + <expand macro="citations" /> +</tool>