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comparison sim.xml @ 11:807aa4c9293d draft

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"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
comparison
equal deleted inserted replaced
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