def main():
# For 0 dna systems
trials = ['a' ,'b', 'c']
#constants = [50, 500]
constants = [125, 250]
i = 0
for constant in constants:
for trial in trials:
change_dir = os.path.join(
base_dir, '6dna', 'k{}_{}'.format(constant,trial))
if not os.path.isdir(change_dir):
os.makedirs(change_dir)
os.chdir(change_dir)
shutil.copyfile(os.path.join(input_dir, 'em.mdp'), './em.mdp')
shutil.copyfile(os.path.join(input_dir, 'bilayer-graphene-dna-water-ions.gro'), './bilayer-graphene-dna-water-ions.gro')
shutil.copyfile(os.path.join(input_dir, 'index.ndx'), './index.ndx')
shutil.copyfile(os.path.join(input_dir, 'topol.top'), './topol.top')
with open('angled_insertion.mdp', 'w') as f:
_write_mdp(f, k=constant, seed=randint(100))
with open('submit.pbs', 'w') as f:
lines = 'cd {} \n'.format(change_dir)
lines += 'gmx grompp -f em.mdp -c bilayer-graphene-dna-water-ions.gro -p topol.top -o em -maxwarn 1\n'
lines += 'gmx mdrun -deffnm em \n'
lines += 'gmx grompp -f angled_insertion.mdp -c em.gro -p topol.top -maxwarn 1 -n index.ndx -o pull \n'
lines += 'gmx mdrun -ntomp 8 -ntmpi 2 -gpu_id 01 -deffnm pull \n'
script_utils.write_rahman_script(f,
jobname='6dna_k{}_{}'.format(constant,trial),
body=lines)
operations.submit_job('submit.pbs', jobid, n_nodes, i)
i += 1
box=system.boundingbox,
overwrite=True,
residues=set([p.parent.name for p in system.particles()]))
system.save('compound.gro',
box=system.boundingbox,
overwrite=True,
residues=set([p.parent.name for p in system.particles()]))
bilayer.write_gmx_topology(system, 'compound.top', header=path_to_ff)
# EQ sims
p = subprocess.Popen('cp ~/Programs/setup/Bilayer/mdp_charmm/*.mdp .',
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
p.wait()
with open('eq.pbs', 'w') as f:
body = 'cd {}\n'.format(os.getcwd())
body += 'module load gromacs/2018.1\n'
body += operations.write_eq_lines(gro='compound.gro',
top='compound.top')
script_utils.write_rahman_script(f,
jobname="{}_setup".format(name),
body=body)
jobid = operations.submit_job('eq.pbs', jobid, n_nodes, i)
os.chdir(curr_dir)
with open('index.txt', 'w') as f:
json.dump(index, f, indent=2)
import os
import itertools as it
import script_utils
from operations import submit_job, compute_work, compute_penetration
from multiprocessing import Pool
n_nodes = 2
jobid = [None] * n_nodes
i = 0
curr_dir = os.getcwd()
#sds_folders = ['10sds', '20sds', '30sds', '40sds', '50sds', '60sds']
sds_folders = ['100sds']
k_folders = ['k50']
angle_folders = ['0']
trials = ['a', 'b', 'c']
for combo in it.product(sds_folders, k_folders, angle_folders, trials):
sim_dir = os.path.join(curr_dir, '{0}/{1}_{2}_{3}'.format(*combo))
print("{}".format(sim_dir))
if os.path.isdir(sim_dir):
os.chdir(sim_dir)
if os.path.isfile('pull.tpr') and not os.path.isfile('pull.gro'):
cmd = 'cd {}\n'.format(sim_dir)
cmd += 'gmx mdrun -deffnm pull -ntomp 8 -ntmpi 2 -gpu_id 01 -append -cpi pull_prev.cpt -pf pull_pullf.xvg -px pull_pullx.xvg \n'
with open('pull.pbs', 'w') as f:
script_utils.write_rahman_script(
f, jobname='{0}_{3}'.format(*combo), body=cmd)
submit_job('pull.pbs', jobid, n_nodes, i)
i += 1
import os
import json
import numpy as np
import operations
import script_utils
################
## Script to iterate through folders, write rwmd files, and submit
################
index = json.load(open('index.txt', 'r'))
n_nodes = 3
jobid = [None] * n_nodes
curr_dir = os.getcwd()
for i, name in enumerate(index.keys()):
os.chdir(os.path.join(curr_dir, name))
rwmd_submission = operations.write_rwmd_lines(
tc_groups=['non-water', 'water'],
t_pairs=[[305, 455], [305, 455]],
cooling_rate=1000,
gro='npt_500ps.gro',
top='compound.top')
with open('rwmd_chain.pbs', 'w') as f:
body = 'cd {}\n'.format(os.getcwd())
body += rwmd_submission
script_utils.write_rahman_script(f,
jobname='{}_rwmd'.format(name),
body=body)
jobid = operations.submit_job('rwmd_chain.pbs', jobid, n_nodes, i)
import os
import json
import numpy as np
import operations
import script_utils
################
## Script to iterate through folders, write production files, and submit
################
index = json.load(open('index.txt', 'r'))
n_nodes = 3
jobid = [None] * n_nodes
curr_dir = os.getcwd()
for i, name in enumerate(index.keys()):
os.chdir(os.path.join(curr_dir, name))
lines = operations.write_production_lines(filename='npt')
with open('production.pbs', 'w') as f:
body = 'cd {}\n'.format(os.getcwd())
body += lines
script_utils.write_rahman_script(f,
jobname='{}_production'.format(name),
body=body)
jobid = operations.submit_job('production.pbs', jobid, n_nodes, i)
import os
import operations
import script_utils
folders = ['trial4', 'trial5', 'trial6']
main_dir = os.getcwd()
jobids = [None] * 2
for i, folder in enumerate(folders):
os.chdir(os.path.join(main_dir, folder))
body = 'cd {}\n'.format(os.getcwd())
body += "gmx mdrun -ntomp 8 -ntmpi 2 -gpu_id 01 -deffnm npt"
with open('submit.pbs', 'w') as f:
script_utils.write_rahman_script(
f, jobname="graphene_agg_{}".format(folder), body=body)
operations.submit_job('submit.pbs', jobids, 2, i)