Mercurial > repos > chemteam > gmx_sim
comparison sim.xml @ 11:807aa4c9293d draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit ab7232ec03a3361f808f5a0be0828e0f7fbd376d"
| author | chemteam |
|---|---|
| date | Mon, 23 Nov 2020 10:48:28 +0000 |
| parents | f197e34c33a9 |
| children | 73008ef1f487 |
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| 10:f197e34c33a9 | 11:807aa4c9293d |
|---|---|
| 41 -n ./index.ndx | 41 -n ./index.ndx |
| 42 #end if | 42 #end if |
| 43 -p ./top_input.top | 43 -p ./top_input.top |
| 44 -o outp.tpr &>> verbose.txt && | 44 -o outp.tpr &>> verbose.txt && |
| 45 | 45 |
| 46 | 46 #if "\${GPU_AVAILABLE:-0}" == 1: |
| 47 gmx mdrun | 47 gmx_gpu mdrun |
| 48 -nt "\${GALAXY_SLOTS:-4}" | |
| 49 ## GPU | |
| 50 #if "\${GROMACS_GPU:-0}" == 1: | |
| 51 -ntmpi 1 | 48 -ntmpi 1 |
| 52 -nb gpu | 49 -nb gpu |
| 53 -pme gpu | 50 -pme gpu |
| 54 #end if | 51 #else: |
| 52 gmx mdrun | |
| 53 #end if | |
| 54 -nt "\${GALAXY_SLOTS:-4}" | |
| 55 -deffnm outp &>> verbose.txt | 55 -deffnm outp &>> verbose.txt |
| 56 | 56 |
| 57 #if $outps.str == 'pdb' or $outps.str == 'both' | 57 #if $outps.str == 'pdb' or $outps.str == 'both' |
| 58 && gmx editconf -f outp.gro -o outp.pdb &>> verbose.txt | 58 && gmx editconf -f outp.gro -o outp.pdb &>> verbose.txt |
| 59 #end if | 59 #end if |