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update to env path

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hotwa
2024-01-03 11:17:37 +08:00
parent 4257c2041a
commit 11a97fb80c
9 changed files with 63 additions and 20 deletions
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md_gromacs.sh
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@@ -261,7 +261,7 @@ gmx_mpi grompp -f ${MDRUN_NAME}.mdp -c npt.gro -t npt.cpt -p topol.top -o ${TPR_
# Run the simulation
gmx_mpi mdrun -deffnm ${MDRUN_NAME}
# mpirun -np $(ls | egrep "Scaled[0-9]+$" | wc -l) gmx_mpi mdrun -v --deffnm md -cpi Scaled.cpt -multidir $(ls -v | egrep "Scaled[0-9]+$") -plumed plumed.dat -hrex -replex 1000 >& run_$(date "+%H%M%S_%d%m%Y").log || { echo "mdrun failed at line ${LINENO} "; exit -1; }
# extra ndx file , select protein
echo -e "1\nq" | gmx_mpi make_ndx -f ${MDRUN_NAME}.gro -o ${NDX_FILE}
# echo -e "1\nq" | gmx_mpi make_ndx -f md.gro -o index.ndx