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Speed tweaks

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This commit is contained in:
Kevin Wu
2023-03-07 15:58:32 -08:00
parent dfd6842643
commit ef740c6d39
1 changed files with 8 additions and 3 deletions
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11
scripts/gromacs/gromacs.py
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@@ -18,6 +18,7 @@ import logging
import shlex
import subprocess
import shutil
import multiprocessing as mp
GRO_FILE_DIR = "/home/wukevin/software/md_template/mdp/"
@@ -85,7 +86,7 @@ def run_gromacs(
# come to "room temperature"
grompp_cmd = f"{gmx} grompp -f {gro_file_dir}nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr"
subprocess.call(shlex.split(grompp_cmd))
nvt_cmd = f"{gmx} mdrun -deffnm nvt"
nvt_cmd = f"{gmx} mdrun -ntmpi 1 -ntomp {mp.cpu_count()} -nb gpu -pin on -deffnm nvt"
subprocess.call(shlex.split(nvt_cmd))
# NPT
@@ -93,13 +94,17 @@ def run_gromacs(
f"{gmx} grompp -f {gro_file_dir}npt.mdp -c nvt.gro -o npt.tpr -p topol.top"
)
subprocess.call(shlex.split(grompp_cmd))
npt_cmd = f"{gmx} mdrun -ntmpi 1 -ntomp 32 -pin on -deffnm npt"
npt_cmd = (
f"{gmx} mdrun -ntmpi 1 -ntomp {mp.cpu_count()} -nb gpu -pin on -deffnm npt"
)
subprocess.call(shlex.split(npt_cmd))
# Production run
grompp_cmd = f"{gmx} grompp -f {gro_file_dir}md.mdp -c npt.gro -t npt.cpt -p topol.top -o prod.tpr"
subprocess.call(shlex.split(grompp_cmd))
prod_cmd = f"{gmx} mdrun -ntmpi 1 -ntomp 32 -pin on -deffnm prod"
prod_cmd = (
f"{gmx} mdrun -ntmpi 1 -ntomp {mp.cpu_count()} -nb gpu -pin on -deffnm prod"
)
subprocess.call(shlex.split(prod_cmd))
# Produce a PDB of final structure