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Update gromacs script to add a constant amount of water

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This commit is contained in:
Kevin Wu
2023-03-30 13:50:45 -07:00
parent c5a557e8fa
commit 106b3632ac
1 changed files with 23 additions and 8 deletions
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31
scripts/gromacs/gromacs.py
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@@ -20,7 +20,12 @@ import subprocess
import shutil
GRO_FILE_DIR = os.path.join(os.path.dirname(__file__), "mdp")
# Up the prod.mdp nsteps to 50000000 to run a longer simulation
# 6nm x 6nm x 6nm (or 7) box (currently gives you 1nm padding around the protein)
# gmx insert-molecules -f <grofile.gro> -ci <spc216.gro> -box <x y z> -nmol <# of waters>
# Run the biggest thing, use box volume and the same number of waters for other things
# Run a bunch of 128 residues and see how many water get added
def run_gromacs(
pdb_file: str,
@@ -46,16 +51,26 @@ def run_gromacs(
p.communicate(input="6".encode())
# gen box - put this in a water solvent 'in a box' - 1nm around the system
box_file = os.path.join(outdir, "box.gro")
box_cmd = f"{gmx} editconf -f {gro_file} -o {box_file} -c -d 1"
subprocess.call(shlex.split(box_cmd))
# box_file = os.path.join(outdir, "box.gro")
# box_cmd = f"{gmx} editconf -f {gro_file} -o {box_file} -c -d 1"
# subprocess.call(shlex.split(box_cmd))
# solvate - add water
solvate_cmd = (
f"{gmx} solvate -cp {box_file} -o solv.gro -cs spc216.gro -p topol.top"
)
logging.debug(f"solvate cmd: {solvate_cmd}")
subprocess.call(shlex.split(solvate_cmd))
# solvate_cmd = (
# f"{gmx} solvate -cp {box_file} -o solv.gro -cs spc216.gro -p topol.top"
# )
# logging.debug(f"solvate cmd: {solvate_cmd}")
# subprocess.call(shlex.split(solvate_cmd))
# Rather than automatically adding a box and solvating, add an explicit constnat number of
# water atoms. This is becasue the energy of the system is dependent on the number of atoms,
# so we hold this constant.
sol_add = 'echo "SOL 12000" >> topol.top'
subprocess.call(sol_add, shell=True)
addwater_cmd = f"{gmx} insert-molecules -f {gro_file} -ci {gro_file_dir}water2.gro -box 12 12 12 -nmol 12000 -o solv.gro"
subprocess.call(shlex.split(addwater_cmd))
# add ions - add counter postive and negative ions to make
# the box "neutral"