From baaf63f83a6fbf25e5374c7735f9eccf5a83456a Mon Sep 17 00:00:00 2001 From: hotwa Date: Tue, 9 Jan 2024 10:10:10 +0800 Subject: [PATCH] add cores args --- md_gromacs.sh | 30 +++++++++++++++++------------- 1 file changed, 17 insertions(+), 13 deletions(-) diff --git a/md_gromacs.sh b/md_gromacs.sh index fb4c444..d91de78 100755 --- a/md_gromacs.sh +++ b/md_gromacs.sh @@ -14,6 +14,8 @@ WATERMODEL=${WATERMODEL:-"tip3p"} WATERTOPFILE=${WATERTOPFILE:-"spc216.gro"} BOXTYPE=${BOXTYPE:-"tric"} BOXORIENTATION=${BOXORIENTATION:-"1.0"} +NUM_CORES=${NUM_CORES:-$(($(nproc) - 2))} # 默认使用 CPU 核心数减去 2，如果外部有设置则使用外部值 +NUM_CORES=$((NUM_CORES > 0 ? NUM_CORES : 1)) # 确保 NUM_CORES 至少为 1 NSTEPS=${NSTEPS:-500000} # 50,000 steps for 1 ns DT=${DT:-0.002} # 2 fs #BOXSIZE="5.0" @@ -48,13 +50,14 @@ echo "XTC_FILE: $XTC_FILE" echo "NO_PBC_XTC_FILE: $NO_PBC_XTC_FILE" echo "OUTPUT_FOLDER: $OUTPUT_FOLDER" echo "EXTRACT_EVERY_PS: $EXTRACT_EVERY_PS" +echo "NUM_CORES: $NUM_CORES" # generate GROMACS .gro file -gmx_mpi pdb2gmx -f $NAME.pdb -o $NAME.gro -ff $FORCEFIELD -water $WATERMODEL -ignh -p topol.top +mpirun -np $NUM_CORES gmx_mpi pdb2gmx -f $NAME.pdb -o $NAME.gro -ff $FORCEFIELD -water $WATERMODEL -ignh -p topol.top # define the box -gmx_mpi editconf -f $NAME.gro -o $NAME-box.gro -bt $BOXTYPE -c -d $BOXORIENTATION +mpirun -np $NUM_CORES gmx_mpi editconf -f $NAME.gro -o $NAME-box.gro -bt $BOXTYPE -c -d $BOXORIENTATION # add solvate -gmx_mpi solvate -cp $NAME-box.gro -cs $WATERTOPFILE -o $NAME-solv.gro -p topol.top +mpirun -np $NUM_CORES gmx_mpi solvate -cp $NAME-box.gro -cs $WATERTOPFILE -o $NAME-solv.gro -p topol.top # add icons # ! ions.mdp add by manual # --- ions.mdp file content --- # cat << EOF > ions.mdp @@ -73,8 +76,9 @@ rcoulomb = 1.0 ; Short-range electrostatic cut-off rvdw = 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions EOF -gmx_mpi grompp -f ions.mdp -c $NAME-solv.gro -p topol.top -o ions.tpr -maxwarn 1 -echo SOL | gmx_mpi genion -s ions.tpr -o $NAME-solv-ions.gro -p topol.top -pname NA -nname CL -conc 0.125 -neutral +mpirun -np $NUM_CORES gmx_mpi grompp -f ions.mdp -c $NAME-solv.gro -p topol.top -o ions.tpr -maxwarn 1 +echo "SOL" > ions_input.txt +mpirun -np $NUM_CORES gmx_mpi genion -s ions.tpr -o $NAME-solv-ions.gro -p topol.top -pname NA -nname CL -conc 0.125 -neutral < ions_input.txt # energy minimization of the structure in solvate # ! minim.mdp add by manual # --- minim.mdp file content --- # cat << EOF > minim.mdp @@ -93,8 +97,8 @@ rcoulomb = 1.0 ; Short-range electrostatic cut-off rvdw = 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions EOF -gmx_mpi grompp -f minim.mdp -c $NAME-solv-ions.gro -p topol.top -o em.tpr -gmx_mpi mdrun -v -deffnm em +mpirun -np $NUM_CORES gmx_mpi grompp -f minim.mdp -c $NAME-solv-ions.gro -p topol.top -o em.tpr +mpirun -np $NUM_CORES gmx_mpi mdrun -v -deffnm em # optional em, you will need the Xmgrace plotting too #gmx_mpi energy -f em.edr -o potential.xvg #position restrain @@ -146,8 +150,8 @@ gen_vel = yes ; assign velocities from Maxwell distributio gen_temp = 300 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed EOF -gmx_mpi grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr -gmx_mpi mdrun -v -deffnm nvt +mpirun -np $NUM_CORES gmx_mpi grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr +mpirun -np $NUM_CORES gmx_mpi mdrun -v -deffnm nvt # optional : Let's analyze the temperature progression, again using energy: # gmx_mpi energy -f nvt.edr -o temperature.xvg # npt @@ -199,8 +203,8 @@ pbc = xyz ; 3-D PBC ; Velocity generation gen_vel = no ; Velocity generation is off EOF -gmx_mpi grompp -f npt.mdp -c nvt.gro -r nvt.gro -t nvt.cpt -p topol.top -o npt.tpr -gmx_mpi mdrun -v -deffnm npt +mpirun -np $NUM_CORES gmx_mpi grompp -f npt.mdp -c nvt.gro -r nvt.gro -t nvt.cpt -p topol.top -o npt.tpr +mpirun -np $NUM_CORES gmx_mpi mdrun -v -deffnm npt # Optional: Let's analyze the pressure progression, again using energy: type 18 0 # gmx energy -f npt.edr -o pressure.xvg # Optional: Let's take a look at density as well, this time using energy and entering "24 0" at the prompt. @@ -257,10 +261,10 @@ gen_vel = no ; Velocity generation is off EOF # Generate GROMACS .tpr file for the simulation -gmx_mpi grompp -f ${MDRUN_NAME}.mdp -c npt.gro -t npt.cpt -p topol.top -o ${TPR_FILE} +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 -gmx_mpi mdrun -deffnm ${MDRUN_NAME} +mpirun -np $NUM_CORES 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}