annotate minim.xml @ 14:d532b7e5f64b draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3"

<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
                    gen-seed  = $mdp.seed              ; random seed

                    ; 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." />
                <param argument="seed" type="integer" label="Random seed" value="1" min="-1" help="Select a random seed for initial velocity generation. Set to -1 to generate a seed." />
            </when>
        </conditional>
        <expand macro="log" />
    </inputs>
    <outputs>
        <data name="output1" format="gro" from_work_dir="em.gro" label="GROMACS energy minimization (GRO) on ${on_string}"/>
        <data name="output2" format="edr" from_work_dir="em.edr" label="GROMACS energy minimization (EDR) on ${on_string}"/>
        <expand macro="log_outputs" />
    </outputs>
    <tests>
        <test>
            <param name="gro_input" value="str_ions.gro" />
            <param name="top_input" value="topol_md.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" file="minim.gro" ftype="gro" lines_diff="20" />
            <output name="output2" ftype="edr" >
                <assert_contents>
                    <has_size value="5644"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="gro_input" value="str_ions.gro" />
            <param name="top_input" value="topol_md.top" />
            <param name="mdpfile" value="custom" />
            <param name="mdp_input" value="minim.mdp" />
            <output name="output1" file="minim.gro" ftype="gro" lines_diff="20" />
            <output name="output2" ftype="edr" >
                <assert_contents>
                    <has_size value="5644"/>
                </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>