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comparison minim.xml @ 15:59c662ca4211 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit bf18581ac3de6b65bdc0a988e6f844cea6e77975"
author chemteam
date Wed, 27 Oct 2021 07:59:52 +0000
parents d532b7e5f64b
children aeec3c2719da
comparison
equal deleted inserted replaced
14:d532b7e5f64b 15:59c662ca4211
1 <tool id="gmx_em" name="GROMACS energy minimization" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> 1 <tool id="gmx_em" name="GROMACS energy minimization" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
2 <description>of the system prior to equilibration and production MD</description> 2 <description>of the system prior to equilibration and production MD</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <token name="@GALAXY_VERSION@">0</token> 5 <token name="@GALAXY_VERSION@">1</token>
6 </macros> 6 </macros>
7 7
8 <expand macro="requirements" /> 8 <expand macro="requirements" />
9 9
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
16 #end if 16 #end if
17 17
18 ln -s '$gro_input' ./solv_ions.gro && 18 ln -s '$gro_input' ./solv_ions.gro &&
19 ln -s '$top_input' ./top_input.top && 19 ln -s '$top_input' ./top_input.top &&
20 20
21 gmx grompp -f ./minim.mdp -c ./solv_ions.gro -r ./solv_ions.gro -p ./top_input.top -o em.tpr &>> verbose.txt && 21 gmx grompp -f ./minim.mdp -c ./solv_ions.gro -r ./solv_ions.gro -p ./top_input.top -o em.tpr @MAXWARN_CMD@ &>> verbose.txt &&
22 gmx mdrun -nt "\${GALAXY_SLOTS:-4}" -deffnm em &>> verbose.txt 22 gmx mdrun -nt "\${GALAXY_SLOTS:-4}" -deffnm em &>> verbose.txt
23 23
24 ]]></command> 24 ]]></command>
25 <configfiles> 25 <configfiles>
26 <!-- .mdp files for the gromacs simulation --> 26 <!-- .mdp files for the gromacs simulation -->
80 <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" /> 80 <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" />
81 <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." /> 81 <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." />
82 <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." /> 82 <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." />
83 </when> 83 </when>
84 </conditional> 84 </conditional>
85 <expand macro="maxwarn" />
85 <expand macro="log" /> 86 <expand macro="log" />
86 </inputs> 87 </inputs>
87 <outputs> 88 <outputs>
88 <data name="output1" format="gro" from_work_dir="em.gro" label="GROMACS energy minimization (GRO) on ${on_string}"/> 89 <data name="output1" format="gro" from_work_dir="em.gro" label="GROMACS energy minimization (GRO) on ${on_string}"/>
89 <data name="output2" format="edr" from_work_dir="em.edr" label="GROMACS energy minimization (EDR) on ${on_string}"/> 90 <data name="output2" format="edr" from_work_dir="em.edr" label="GROMACS energy minimization (EDR) on ${on_string}"/>