Mercurial > repos > chemteam > gmx_em
comparison minim.xml @ 15:59c662ca4211 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit bf18581ac3de6b65bdc0a988e6f844cea6e77975"
author | chemteam |
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date | Wed, 27 Oct 2021 07:59:52 +0000 |
parents | d532b7e5f64b |
children | aeec3c2719da |
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14:d532b7e5f64b | 15:59c662ca4211 |
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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}"/> |