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use GPU mdrun

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lingyuzeng
2024-02-22 11:02:40 +08:00
parent 5e3198957b
commit fb32029a61
1 changed files with 1 additions and 1 deletions
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md_gromacs.sh
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@@ -281,7 +281,7 @@ EOF
# Generate GROMACS .tpr file for the simulation
run_command "Preparing MD simulation" "mpirun -np $NUM_CORES gmx_mpi grompp -f ${MDRUN_NAME}.mdp -c npt.gro -t npt.cpt -p topol.top -o ${TPR_FILE}"
# Run the simulation
mpirun -np $NUM_CORES gmx_mpi mdrun -deffnm ${MDRUN_NAME}
mpirun -np ${NUM_CORES} gmx_mpi mdrun -deffnm ${MDRUN_NAME} -update gpu -ntomp 1
# 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}