Mercurial > repos > chemteam > gmx_solvate
diff solvate.xml @ 4:cdacad684da1 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 10f45d117e34624bceb32442742ae0b8eb2dae30"
author | chemteam |
---|---|
date | Wed, 30 Oct 2019 13:32:37 -0400 |
parents | 7161b230adad |
children | 645139abefae |
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--- a/solvate.xml Mon Oct 07 12:47:31 2019 -0400 +++ b/solvate.xml Wed Oct 30 13:32:37 2019 -0400 @@ -14,7 +14,7 @@ gmx solvate -cp ./gro_input.gro -cs ${water_model}.gro -o solv.gro -p ./top_input.top &>> verbose.txt && - gmx grompp -f ./ions.mdp -c solv.gro -p ./top_input.top -o ions.tpr -maxwarn 1 &>> verbose.txt && + gmx grompp -f ./ions.mdp -c solv.gro -p ./top_input.top -o ions.tpr &>> verbose.txt && echo 'SOL' | gmx genion -s ions.tpr -o solv_ions.gro -p ./top_input.top -pname NA -nname CL -neutral &>> verbose.txt @@ -30,7 +30,7 @@ nstlist = 1 cutoff-scheme = Verlet ns_type = grid -coulombtype = PME +coulombtype = cutoff rcoulomb = 1.0 rvdw = 1.0 pbc = xyz @@ -39,10 +39,10 @@ <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"> - <option value="tip3p">TIP3P</option> - <option value="tip4p">TIP4P</option> - <option value="spc216">SPC</option> + <param name="water_model" type="select" label="Water model for solvation" help="Note SPC is a generic equilibrated 3-point solvent model and can be used as the solvent configuration for any of SPC, SPC/E, or TIP3P water."> + <option value="spc216" selected="true">SPC (generic three-point model)</option> + <option value="tip4p">TIP4P (four-point model)</option> + <option value="tip5p">TIP5P (five-point model)</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."/>