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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit ab7232ec03a3361f808f5a0be0828e0f7fbd376d"
author | chemteam |
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date | Mon, 23 Nov 2020 10:47:01 +0000 |
parents | 55918daa5651 |
children | d532b7e5f64b |
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<tool id="gmx_em" name="GROMACS energy minimization" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> <description>of the system prior to equilibration and production MD</description> <macros> <import>macros.xml</import> <token name="@GALAXY_VERSION@">0</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ #if $mdp.mdpfile == 'custom': ln -s '$mdp.mdp_input' ./minim.mdp && #else: ln -s '$minim' ./minim.mdp && #end if ln -s '$gro_input' ./solv_ions.gro && ln -s '$top_input' ./top_input.top && gmx grompp -f ./minim.mdp -c ./solv_ions.gro -r ./solv_ions.gro -p ./top_input.top -o em.tpr &>> verbose.txt && gmx mdrun -nt "\${GALAXY_SLOTS:-4}" -deffnm em &>> verbose.txt ]]></command> <configfiles> <!-- .mdp files for the gromacs simulation --> <configfile name="minim"> #if $mdp.mdpfile == 'default': ; minim.mdp - used as input into grompp to generate em.tpr integrator = $mdp.integrator ; Algorithm (steep = steepest descent minimization) emtol = $mdp.emtol ; Stop minimization when the maximum force is less than this value emstep = $mdp.emstep ; Energy step size nsteps = $mdp.md_steps ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = $mdp.cutoffscheme ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = $mdp.coulombtype ; Treatment of long range electrostatic interactions 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 pbc = xyz ; Periodic Boundary Conditions (yes/no) #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="mdp"> <param name="mdpfile" type="select" label="Parameter input"> <option value="custom">Upload own MDP file</option> <option value="default">Use default (partially customisable) setting</option> </param> <when value="custom"> <param argument="mdp_input" type="data" format='mdp' label="MD parameters (MDP) file (optional; default settings if not set)."/> </when> <when value="default"> <param argument="integrator" type="select" label="Choice of integrator."> <option value="steep">Steepest descent algorithm.</option> <option value="cg">Conjugate gradient algorithm.</option> <option value="l-bfgs">Quasi-Newtonian algorithm.</option> </param> <param argument="cutoffscheme" type="select" label="Neighbor searching."> <option value="Verlet">Generate a pair list with buffering.</option> <option value="group">Generate a pair list for groups of atoms.</option> </param> <param argument="coulombtype" type="select" label="Electrostatics."> <option value="PME">Fast smooth Particle-Mesh Ewald (SPME) electrostatics.</option> <option value="P3M-AD">Particle-Particle Particle-Mesh algorithm with analytical derivative.</option> <option value="Reaction-Field-zero">Reaction field electrostatics.</option> </param> <param argument="rcoulomb" value="1.0" type="float" label="Distance for the Coulomb cut-off."/> <param argument="rlist" value="1.0" type="float" label="Cut-off distance for the short-range neighbor list. Ignored if the Verlet cutoff scheme is set."/> <param argument="rvdw" value="1.0" type="float" label="Short range van der Waals cutoff."/> <param argument="md_steps" type="integer" label="Number of steps for the MD simulation" value="0" min="0" max="1000000" help="MD steps" /> <param argument="emtol" type="float" label="EM tolerance" value="0" min="0" max="10000" help="The minimization is converged when the maximum force is smaller than this value" /> <param argument="emstep" type="float" label="Maximum step size /nm" value="0.01" min="0.0001" max="1.0" help="Initial step size in nm." /> </when> </conditional> <expand macro="log" /> </inputs> <outputs> <data name="output1" format="gro" from_work_dir="em.gro"/> <data name="output2" format="edr" from_work_dir="em.edr"/> <expand macro="log_outputs" /> </outputs> <tests> <test> <param name="gro_input" value="str_ions.gro" /> <param name="top_input" value="topol_solv.top" /> <param name="mdpfile" value="default" /> <param name="integrator" value="steep" /> <param name="cutoffscheme" value="Verlet" /> <param name="coulombtype" value="PME" /> <param name="rcoulomb" value="1.0" /> <param name="rlist" value="1.0" /> <param name="md_steps" value="50000" /> <param name="emtol" value="1000.0" /> <param name="emstep" value="0.01" /> <output name="output1" ftype="gro" > <assert_contents> <has_size value="4281" /> </assert_contents> </output> <output name="output2" ftype="edr" > <assert_contents> <!-- this binary can vary in size a lot unfortunately --> <has_size value="5000" delta="1000" /> </assert_contents> </output> </test> <test> <param name="gro_input" value="str_ions.gro" /> <param name="top_input" value="topol_solv.top" /> <param name="mdpfile" value="custom" /> <param name="mdp_input" value="minim.mdp" /> <output name="output1" ftype="gro" > <assert_contents> <has_size value="4281" /> </assert_contents> </output> <output name="output2" ftype="edr" > <assert_contents> <!-- this binary can vary in size a lot unfortunately --> <has_size value="5000" delta="1000" /> </assert_contents> </output> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** This tool performs energy minimization of a system prior to a GROMACS simulation. _____ .. class:: infomark **Input** - GRO structure file. - Topology (TOP) file. - MDP parameter file (optional) To take advantage of all GROMACS features, upload an MDP file with simulation parameters. Otherwise, choose parameters through the Galaxy interface. See the `manual`_ for more information on the options. .. _`manual`: http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html _____ .. class:: infomark **Output** - GRO structure file. ]]></help> <expand macro="citations" /> </tool>