diff --git a/script/S112D.sh b/script/S112D.sh index 9b03970..ea5fefa 100644 --- a/script/S112D.sh +++ b/script/S112D.sh @@ -8,6 +8,7 @@ if [ -n "$GMXRC_PATH" ]; then source "$GMXRC_PATH" # source /home/lingyuzeng/software/gmx2023.2/bin/GMXRC fi +GPU_ID=${GPU_ID:-"0"} NAME=${NAME:-"S112D-Alphafold2"} # FORCEFIELD=${FORCEFIELD:-"amber99sb-ildn"} FORCEFIELD=${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} # 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 echo -e "1\nq" | gmx_mpi make_ndx -f ${MDRUN_NAME}.gro -o ${NDX_FILE}