Mercurial > repos > chemteam > gmx_sim
diff sim.xml @ 2:5642f48f5698 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
| author | chemteam |
|---|---|
| date | Wed, 20 Nov 2019 11:13:22 -0500 |
| parents | ec3f665cca3e |
| children | 4dba9a5b74fc |
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--- a/sim.xml Wed Oct 30 13:34:07 2019 -0400 +++ b/sim.xml Wed Nov 20 11:13:22 2019 -0500 @@ -5,47 +5,48 @@ </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ - #if $mdp.mdpfile == "custom": - ln -s '$mdp.mdp_input' ./md.mdp && + + #if $sets.mdp.mdpfile == "custom": + ln -s '$sets.mdp.mdp_input' ./md.mdp && #end if - #if $mdp.mdpfile == "default": + #if $sets.mdp.mdpfile == "default": ln -s '$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 && + #if $inps.itp_in: + ln -s '$inps.itp_in' ./posres.itp && #end if - #if $ndx_inp.ndx_bool == "yes": - ln -s '$ndx_inp.ndx_in' ./index.ndx && + #if $inps.cpt_in: + ln -s '$inps.cpt_in' ./inp.cpt && + #end if + + #if $inps.ndx_in: + ln -s '$inps.ndx_in' ./index.ndx && #end if gmx grompp -f ./md.mdp -c ./inp.gro - #if $cpt_inp.cpt_bool == "yes": - -t ./inp.cpt + #if $inps.cpt_in: + -t ./inp.cpt #end if - #if $posres.posres_bool == "true": + #if $inps.itp_in: -r ./inp.gro #end if - #if $ndx_inp.ndx_bool == "true": + #if $inps.ndx_in: -n ./index.ndx #end if -p ./top_input.top -o outp.tpr &>> verbose.txt && - - + + gmx mdrun -deffnm outp &>> verbose.txt - #if $str == 'pdb' or $str == 'both' + #if $outps.str == 'pdb' or $outps.str == 'both' && gmx editconf -f outp.gro -o outp.pdb &>> verbose.txt #end if @@ -55,42 +56,44 @@ <configfiles> <!-- .mdp file for the gromacs simulation --> <configfile name="md"> - #if $mdp.mdpfile == 'default': + #if $sets.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 + integrator = $sets.mdp.integrator ; leap-frog integrator + nsteps = $sets.mdp.md_steps ; 2 * 500000 = 1000 ps (1 ns) + dt = $sets.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 = $sets.mdp.write_freq ; save coordinates every 10.0 ps + nstvout = $sets.mdp.write_freq ; save velocities every 10.0 ps + nstenergy = $sets.mdp.write_freq ; save energies every 10.0 ps + nstlog = $sets.mdp.write_freq ; update log file every 10.0 ps + nstxout-compressed = $sets.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 + #if $inps.cpt_in: + continuation = yes ; Restarting after NPT + #end if constraint_algorithm = lincs ; holonomic constraints - constraints = $mdp.constraints ; all bonds (even heavy atom-H bonds) constrained + constraints = $sets.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 + cutoff-scheme = $sets.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 + rcoulomb = $sets.mdp.rcoulomb ; Short-range electrostatic cut-off + rlist = $sets.mdp.rlist ; Cut-off distance for the short-range neighbor list. + rvdw = $sets.mdp.rvdw ; Short-range Van der Waals cut-off ; Electrostatics - coulombtype = $mdp.coulombtype ; method for electrostatics calculations e.g. PME + coulombtype = $sets.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 + ref_t = $sets.mdp.temperature $sets.mdp.temperature ; reference temperature, one for each group, in K ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction @@ -98,11 +101,11 @@ ; Velocity generation gen_vel = no ; Velocity generation is off #end if - #if $posres.posres_bool == "true": + #if $inps.itp_in: define = -DPOSRES ; position restrain the protein refcoord_scaling = com #end if - #if $ensemble == "nvt": + #if $sets.ensemble == "nvt": pcoupl = no ; no pressure coupling in NVT #else: ; Pressure coupling is on @@ -119,101 +122,168 @@ <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> + + <section name="inps" title="Inputs" expanded="false"> + + <!-- CPT inp --> + <!-- <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 argument="cpt_in" type="data" format='cpt' label="Checkpoint (CPT) file" optional="true" help="CPT file from a previous MD run. Leave empty if no checkpoint should be used."/> - <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> + <!-- ITP inp --> + <!-- <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_in" type="data" format='itp' label="Position restraint (ITP) file"/> + </when> + <when value="false"/> + </conditional> --> + + <param argument="itp_in" type="data" format='itp' label="Position restraint (ITP) file" optional="true" help="Apply position restraints using a ITP file. Leave empty if no position restraints should be used."/> + + <!-- NDX inp --> + <!-- <conditional name="ndx_inp"> + <param name="ndx_bool" type="select" label="Use a custom index (ndx) file" help="Use an index file specifying custom atom groups."> + <option value="true">Use custom index file</option> + <option value="false" selected="true">Use default generated group</option> + </param> + <when value="true"> + <param argument="ndx_in" type="data" format='ndx' label="Index file"/> + </when> + <when value="false"/> + </conditional> --> + + <param argument="ndx_in" type="data" format='ndx' label="Index (ndx) file" optional="true" help="Use an index file specifying custom atom groups. Leave empty to use default generated group"/> + + </section> + + <section name="outps" title="Outputs" expanded="false"> + <!-- TRAJ out --> + <param argument="traj" type="select" label="Trajectory output"> + <option value='none'>Return no trajectory output</option> + <option value='xtc'>Return .xtc file (reduced precision)</option> + <option value='trr'>Return .trr file (full precision)</option> + <option value='both'>Return both .xtc and .trr files</option> </param> - <when value="true"> - <param argument="itp_inp" type="data" format='itp' label="Position restraint (ITP) file"/> - </when> - <when value="false"/> - </conditional> - <conditional name="ndx_inp"> - <param name="ndx_bool" type="select" label="Use a custom index (ndx) file" help="Use an index file specifying custom atom groups."> - <option value="yes">Use custom index file</option> - <option value="no" selected="true">Use default generated group</option> + <!-- STR out --> + <param argument="str" type="select" label="Structure output"> + <option value='none'>Return no structure output</option> + <option value='gro'>Return .gro file</option> + <option value='pdb'>Return .pdb file</option> + <option value='both'>Return both .gro and .pdb files</option> + </param> + + <!-- CPT out --> + <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> + + <!-- EDR out --> + <param name="edr_out" type="select" label="Produce an energy (EDR) file" help="Produce file containing energies associated with the simulation"> + <option value="true">Produce EDR output</option> + <option value="false" selected="true">No EDR output</option> </param> - <when value="yes"> - <param argument="ndx_in" type="data" format='txt' label="Index file"/> - </when> - <when value="no"/> - </conditional> + <!-- XVG out --> + <param name="xvg_out" type="select" label="Produce XVG output" help="Produce tabular XVG file (e.g. forces from pulling simulations)" > + <option value="true">Produce XVG output</option> + <option value="false" selected="true">No XVG output</option> + </param> + + </section> - <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> + <section name="sets" title="Settings" expanded="false"> + <!-- other ... --> + <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"/> + <expand macro="md_inputs"/> + </section> + + <expand macro="log" /> + </inputs> <outputs> <data name="output1" format="gro" from_work_dir="outp.gro"> - <filter>str == 'gro' or str == 'both'</filter> + <filter>outps.str == 'gro' or outps.str == 'both'</filter> </data> <data name="output2" format="pdb" from_work_dir="outp.pdb"> - <filter>str == 'pdb' or str == 'both'</filter> + <filter>outps.str == 'pdb' or outps.str == 'both'</filter> </data> <data name="output3" format="trr" from_work_dir="outp.trr"> - <filter>traj == 'trr' or traj == 'both'</filter> + <filter>outps.traj == 'trr' or outps.traj == 'both'</filter> </data> <data name="output4" format="xtc" from_work_dir="outp.xtc"> - <filter>traj == 'xtc' or traj == 'both'</filter> + <filter>outps.traj == 'xtc' or outps.traj == 'both'</filter> </data> <data name="output5" format="cpt" from_work_dir="outp.cpt"> - <filter>cpt_out</filter> + <filter>outps.cpt_out == 'true'</filter> + </data> + <data name="output6" format="edr" from_work_dir="outp.edr"> + <filter>outps.edr_out == 'true'</filter> </data> + <collection name="output7" type="list"> + <discover_datasets pattern="(?P<designation>.*)\.xvg" visible="true" directory="." /> + <filter>outps.xvg_out == 'true'</filter> + </collection> - <data name="report" format="txt" from_work_dir="verbose.txt"> - <filter>capture_log</filter> - </data> + <expand macro="log_outputs" /> </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_bool" value="yes" /> --> <param name="cpt_in" value="npt.cpt" /> <param name="mdpfile" value="custom" /> <param name="mdp_input" value="md.mdp" /> - <param name="ndx_bool" value="no" /> + <!-- <param name="ndx_bool" value="false" /> --> <param name="traj" value="trr"/> <param name="str" value="gro"/> <param name="ensemble" value="npt" /> - <param name="posres_bool" value="false" /> + <!-- <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"/> + <!-- <output name="output1" ftype="gro"> + <assert_contents> + <has_size value="2647999" /> + </assert_contents> + </output> + <output name="output3" ftype="trr"> + <assert_contents> + <has_size value="10132584" /> + </assert_contents> + </output> --> </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_bool" value="yes" /> --> <param name="cpt_in" value="npt.cpt" /> - <param name="ndx_bool" value="no" /> + <!-- <param name="ndx_bool" value="false" /> --> <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" /> + <!-- <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"/> @@ -222,15 +292,15 @@ <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_bool" value="yes" /> --> <param name="cpt_in" value="npt.cpt" /> - <param name="ndx_bool" value="yes" /> + <!-- <param name="ndx_bool" value="true" /> --> <param name="ndx_in" value="index.ndx" /> <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" /> + <!-- <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"/> @@ -239,11 +309,11 @@ <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="posres_bool" value="true" /> --> + <param name="itp_in" value="posres.itp" /> + <!-- <param name="cpt_bool" value="no" /> --> <param name="cpt_out" value="true" /> - <param name="ndx_bool" value="no" /> + <!-- <param name="ndx_bool" value="false" /> --> <param name="traj" value="xtc"/> <param name="str" value="pdb"/> <param name="ensemble" value="nvt" />