Mercurial > repos > chemteam > gmx_solvate
changeset 3:7161b230adad draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
| author | chemteam |
|---|---|
| date | Mon, 07 Oct 2019 12:47:31 -0400 |
| parents | b37a1d7bf6c2 |
| children | cdacad684da1 |
| files | macros.xml solvate.xml |
| diffstat | 2 files changed, 52 insertions(+), 28 deletions(-) [+] |
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--- a/macros.xml Fri Aug 30 15:03:34 2019 -0400 +++ b/macros.xml Mon Oct 07 12:47:31 2019 -0400 @@ -1,8 +1,8 @@ <macros> - <token name="@VERSION@">2019.1</token> + <token name="@VERSION@">2019.1.1</token> <xml name="requirements"> <requirements> - <requirement type="package" version="@VERSION@">gromacs</requirement> + <requirement type="package" version="2019.1">gromacs</requirement> </requirements> </xml> <xml name="citations"> @@ -11,32 +11,46 @@ </citations> </xml> <xml name="md_inputs"> + <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> + + <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> + <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)."/> + <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."> + <param argument="integrator" type="select" label="Choice of integrator"> <option value="md">A leap-frog algorithm for integrating Newton's equations of motion.</option> <option value="sd">Stochastic dynamics integrator</option> <option value="bd">An Euler integrator for Brownian or position Langevin dynamics.</option> </param> - <param argument="constraints" type="select" label="Bond constraints (constraints)."> + <param argument="constraints" type="select" label="Bond constraints (constraints)"> <option value="none">No constraints except for those defined explicitly in the topology (none).</option> <option value="h-bonds">Bonds with H-atoms. (h-bonds).</option> <option value="all-bonds">All bonds (all-bonds).</option> <option value="h-angles">Bonds and angles with H-atoms. (h-angles).</option> <option value="all-angles">All bonds and angles (all-angles).</option> </param> - <param argument="cutoffscheme" type="select" label="Neighbor searching."> + <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."> + <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> @@ -48,27 +62,13 @@ <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 NPT equilibration" value="0" min="0" max="1000000" help="NPT steps" /> + <param argument="md_steps" type="integer" label="Number of steps for the simulation" value="0" min="0" max="1000000" help="NPT steps" /> </when> </conditional> - - <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> - <param argument="str" type="select" label="Structure output."> - <option value='none'>Return no trajectory 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> - - <param name="capture_log" type="boolean" value="false" label="Generate Detailed Log" help="Generate detailed log information that can be summarized with ParseLog."/> + <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/> </xml>
--- a/solvate.xml Fri Aug 30 15:03:34 2019 -0400 +++ b/solvate.xml Mon Oct 07 12:47:31 2019 -0400 @@ -37,14 +37,14 @@ </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."/> - <param name="water_model" type="select" label="Water model for solvation."> + <param argument="gro_input" type="data" format='gro' label="GRO structure file"/> + <param argument="top_input" type="data" format='top' label="Topology (TOP) file"/> + <param name="water_model" type="select" label="Water model for solvation"> <option value="tip3p">TIP3P</option> <option value="tip4p">TIP4P</option> <option value="spc216">SPC</option> </param> - <param name="capture_log" type="boolean" value="false" label="Generate Detailed Log" help="Generate detailed log information that can be summarized with ParseLog."/> + <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/> </inputs> <outputs> @@ -65,7 +65,31 @@ </tests> <help><![CDATA[ -Select a water model - consistent with the one selected in system set-up and provide GRO and TOP files to be updated with the added water molecules. In addition, sodium or chloride ions are added if necessary to ensure the system is charge-neutral. +.. class:: infomark + +**What it does** + +This tool solvates a system prior to a GROMACS simulation. In addition, sodium or chloride ions will be added if necessary to ensure the system is charge-neutral. + +_____ + +.. class:: infomark + +**Input** + + - GRO structure file. + - Topology (TOP) file. + +In addition, a water model must be selected - this should be consistent with the one selected previously in the system setup. + +_____ + + +.. class:: infomark + +**Output** + + - GRO structure file. ]]></help>