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comparison solvate.xml @ 4:cdacad684da1 draft

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"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
comparison
equal deleted inserted replaced
3:7161b230adad 4:cdacad684da1
12 ln -s '$gro_input' ./gro_input.gro && 12 ln -s '$gro_input' ./gro_input.gro &&
13 ln -s '$top_input' ./top_input.top && 13 ln -s '$top_input' ./top_input.top &&
14 14
15 gmx solvate -cp ./gro_input.gro -cs ${water_model}.gro -o solv.gro -p ./top_input.top &>> verbose.txt && 15 gmx solvate -cp ./gro_input.gro -cs ${water_model}.gro -o solv.gro -p ./top_input.top &>> verbose.txt &&
16 16
17 gmx grompp -f ./ions.mdp -c solv.gro -p ./top_input.top -o ions.tpr -maxwarn 1 &>> verbose.txt && 17 gmx grompp -f ./ions.mdp -c solv.gro -p ./top_input.top -o ions.tpr &>> verbose.txt &&
18 18
19 echo 'SOL' | gmx genion -s ions.tpr -o solv_ions.gro -p ./top_input.top -pname NA -nname CL -neutral &>> verbose.txt 19 echo 'SOL' | gmx genion -s ions.tpr -o solv_ions.gro -p ./top_input.top -pname NA -nname CL -neutral &>> verbose.txt
20 20
21 ]]></command> 21 ]]></command>
22 <configfiles> 22 <configfiles>
28 emstep = 0.01 28 emstep = 0.01
29 nsteps = 1 29 nsteps = 1
30 nstlist = 1 30 nstlist = 1
31 cutoff-scheme = Verlet 31 cutoff-scheme = Verlet
32 ns_type = grid 32 ns_type = grid
33 coulombtype = PME 33 coulombtype = cutoff
34 rcoulomb = 1.0 34 rcoulomb = 1.0
35 rvdw = 1.0 35 rvdw = 1.0
36 pbc = xyz 36 pbc = xyz
37 </configfile> 37 </configfile>
38 </configfiles> 38 </configfiles>
39 <inputs> 39 <inputs>
40 <param argument="gro_input" type="data" format='gro' label="GRO structure file"/> 40 <param argument="gro_input" type="data" format='gro' label="GRO structure file"/>
41 <param argument="top_input" type="data" format='top' label="Topology (TOP) file"/> 41 <param argument="top_input" type="data" format='top' label="Topology (TOP) file"/>
42 <param name="water_model" type="select" label="Water model for solvation"> 42 <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.">
43 <option value="tip3p">TIP3P</option> 43 <option value="spc216" selected="true">SPC (generic three-point model)</option>
44 <option value="tip4p">TIP4P</option> 44 <option value="tip4p">TIP4P (four-point model)</option>
45 <option value="spc216">SPC</option> 45 <option value="tip5p">TIP5P (five-point model)</option>
46 </param> 46 </param>
47 <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/> 47 <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/>
48 48
49 </inputs> 49 </inputs>
50 <outputs> 50 <outputs>