| Previous changeset 0:5f136e371f44 (2019-11-18) |
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Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit eefe89bfcd6c3e98f4e774e508ad0659dcc2f65c" |
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modified:
alchemical_run/gmx_fep.sh |
| b |
| diff -r 5f136e371f44 -r c1fa72716efc alchemical_run/gmx_fep.sh --- a/alchemical_run/gmx_fep.sh Mon Nov 18 09:52:20 2019 -0500 +++ b/alchemical_run/gmx_fep.sh Sun Dec 01 09:47:52 2019 -0500 |
| b |
| @@ -47,7 +47,7 @@ gmx grompp -f $MDP/em_steep_$LAMBDA.mdp -c $FREE_ENERGY/morph.gro -p $FREE_ENERGY/morph.top -o min$LAMBDA.tpr - gmx mdrun -deffnm min$LAMBDA + gmx mdrun -nt "${GALAXY_SLOTS:-4}" -deffnm min$LAMBDA sleep 10 @@ -62,7 +62,7 @@ gmx grompp -f $MDP/nvt_$LAMBDA.mdp -c ../EM/min$LAMBDA.gro -p $FREE_ENERGY/morph.top -o nvt$LAMBDA.tpr - gmx mdrun -deffnm nvt$LAMBDA + gmx mdrun -nt "${GALAXY_SLOTS:-4}" -deffnm nvt$LAMBDA echo "Constant volume equilibration complete." @@ -78,7 +78,7 @@ gmx grompp -f $MDP/npt_$LAMBDA.mdp -c ../NVT/nvt$LAMBDA.gro -p $FREE_ENERGY/morph.top -t ../NVT/nvt$LAMBDA.cpt -o npt$LAMBDA.tpr - gmx mdrun -deffnm npt$LAMBDA + gmx mdrun -nt "${GALAXY_SLOTS:-4}" -deffnm npt$LAMBDA echo "Constant pressure equilibration complete." @@ -94,7 +94,7 @@ gmx grompp -f $MDP/md_$LAMBDA.mdp -c ../NPT/npt$LAMBDA.gro -p $FREE_ENERGY/morph.top -t ../NPT/npt$LAMBDA.cpt -o md$LAMBDA.tpr - gmx mdrun -deffnm md$LAMBDA + gmx mdrun -nt "${GALAXY_SLOTS:-4}" -deffnm md$LAMBDA echo "Production MD complete." @@ -112,4 +112,3 @@ exit; - |