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add gpu_id

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lingyu zeng
2024-09-18 19:31:58 +08:00
parent 82d60391bf
commit f67fb6c270
1 changed files with 2 additions and 1 deletions
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script/S112D.sh
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@@ -8,6 +8,7 @@
if [ -n "$GMXRC_PATH" ]; then if [ -n "$GMXRC_PATH" ]; then
source "$GMXRC_PATH" # source /home/lingyuzeng/software/gmx2023.2/bin/GMXRC source "$GMXRC_PATH" # source /home/lingyuzeng/software/gmx2023.2/bin/GMXRC
fi fi
GPU_ID=${GPU_ID:-"0"}
NAME=${NAME:-"S112D-Alphafold2"} NAME=${NAME:-"S112D-Alphafold2"}
# FORCEFIELD=${FORCEFIELD:-"amber99sb-ildn"} # FORCEFIELD=${FORCEFIELD:-"amber99sb-ildn"}
FORCEFIELD=${FORCEFIELD:-"amber99sb"} FORCEFIELD=${FORCEFIELD:-"amber99sb"}
@@ -262,7 +263,7 @@ EOF
gmx_mpi grompp -f ${MDRUN_NAME}.mdp -c npt.gro -t npt.cpt -p topol.top -o ${TPR_FILE} gmx_mpi grompp -f ${MDRUN_NAME}.mdp -c npt.gro -t npt.cpt -p topol.top -o ${TPR_FILE}
# Run the simulation # Run the simulation
gmx_mpi mdrun -deffnm ${MDRUN_NAME} -update gpu -ntomp 1 gmx_mpi mdrun -deffnm ${MDRUN_NAME} -update gpu -ntomp 1 -gpu_id ${GPU_ID}
# extra ndx file , select protein # 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 ${MDRUN_NAME}.gro -o ${NDX_FILE}