Skip to content
Snippets Groups Projects
Commit 73c13369 authored by cmaffeo2's avatar cmaffeo2
Browse files

Slightly reorganized simulation protocol; added options to mrdna script and... 

Slightly reorganized simulation protocol; added options to mrdna script and simulate.py for using twist in the coarsest step
parent 8dafa9f9
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
bin/mrdna
+ 19
− 4
View file @ 73c13369
#! /usr/bin/env python #! /usr/bin/env python
# -*- coding: utf-8 -*- # -*- coding: utf-8 -*-
import sys
if sys.version_info[0] != 3:
raise Exception("This script must be run with python3")
import argparse import argparse
import re import re
import pathlib import pathlib
from mrdna import __version__ as __version__ from mrdna import __version__ as __version__
from mrdna.simulate import multiresolution_simulation as simulate from mrdna.simulate import multiresolution_simulation as simulate
"""Easy multiresolution simulations of DNA nanotechnology objects using ARBD"""
parser = argparse.ArgumentParser(prog="mrdna", parser = argparse.ArgumentParser(prog="mrdna",
description="""Easy multiresolution simulations of DNA nanotechnology objects using ARBD""") description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
)
parser.add_argument('-o','--output-prefix', type=str, default=None, parser.add_argument('-o','--output-prefix', type=str, default=None,
help="Name for your job's output") help="Name for your job's output")
...@@ -18,6 +25,10 @@ parser.add_argument('-g','--gpu', type=int, default=0, ...@@ -18,6 +25,10 @@ parser.add_argument('-g','--gpu', type=int, default=0,
help='GPU for simulation; check nvidia-smi for availability') help='GPU for simulation; check nvidia-smi for availability')
parser.add_argument('--output-period', type=float, default=1e4, parser.add_argument('--output-period', type=float, default=1e4,
help='Simulation steps between DCD frames') help='Simulation steps between DCD frames')
# parser.add_argument('--minimization-steps', type=float, default=0,
# help='Simulation steps between DCD frames')
parser.add_argument('--coarse-local-twist', action='store_true',
help='Use local twist for coarsest representation?')
parser.add_argument('--coarse-steps', type=float, default=1e7, parser.add_argument('--coarse-steps', type=float, default=1e7,
help='Simulation steps for coarse model (200 fs/step)') help='Simulation steps for coarse model (200 fs/step)')
parser.add_argument('--fine-steps', type=float, default=1e7, parser.add_argument('--fine-steps', type=float, default=1e7,
...@@ -97,17 +108,20 @@ def main(): ...@@ -97,17 +108,20 @@ def main():
job_id = "job-" + prefix, job_id = "job-" + prefix,
directory = args.directory, directory = args.directory,
gpu = args.gpu, gpu = args.gpu,
minimization_output_period = int(args.output_period),
coarse_local_twist = args.coarse_local_twist,
coarse_output_period = int(args.output_period), coarse_output_period = int(args.output_period),
fine_output_period = int(args.output_period), fine_output_period = int(args.output_period),
minimization_steps = 0, # int(args.minimization_steps),
coarse_steps = int(args.coarse_steps), coarse_steps = int(args.coarse_steps),
fine_steps = int(args.fine_steps), fine_steps = int(args.fine_steps),
backbone_scale = args.backbone_scale backbone_scale = args.backbone_scale
) )
simulate( **run_args ) simulate( **run_args )
if __name__ == '__main__': if __name__ == '__main__':
if args.debug: if args.debug:
class Restart(Exception): class Restart(Exception):
...@@ -132,7 +146,8 @@ if __name__ == '__main__': ...@@ -132,7 +146,8 @@ if __name__ == '__main__':
print("\t" + " ".join(args)) print("\t" + " ".join(args))
except SystemExit: except SystemExit:
# In most cases SystemExit does not warrant a post-mortem session. # In most cases SystemExit does not warrant a post-mortem session.
print("The program exited via sys.exit(). Exit status:", end=' ') # print("The program exited via sys.exit(). Exit status:", end=' ')
print("The program exited via sys.exit(). Exit status:")
print(sys.exc_info()[1]) print(sys.exc_info()[1])
except SyntaxError: except SyntaxError:
traceback.print_exc() traceback.print_exc()
......
mrdna/simulate.py
+ 75
− 66
View file @ 73c13369
...@@ -9,24 +9,34 @@ namd="/home/cmaffeo2/development/namd-bin/NAMD_Git-2017-07-06_Linux-x86_64-multi ...@@ -9,24 +9,34 @@ namd="/home/cmaffeo2/development/namd-bin/NAMD_Git-2017-07-06_Linux-x86_64-multi
## TODO: implement replicas, initial conditions specified through some restart, and a custom simulation schedule ## TODO: implement replicas, initial conditions specified through some restart, and a custom simulation schedule
def multiresolution_simulation( model, output_name, def multiresolution_simulation( model, output_name,
job_id=None, job_id=None,
gpu = 0, gpu = 0,
directory=None, directory=None,
minimization_steps = 0,
coarse_steps = 5e7, coarse_steps = 5e7,
fine_steps = 5e7, fine_steps = 5e7,
minimization_output_period = 1e5,
coarse_output_period = 1e5, coarse_output_period = 1e5,
fine_output_period = 1e5, fine_output_period = 1e5,
coarse_local_twist = False,
remove_long_bonds=False, remove_long_bonds=False,
backbone_scale=1.0, backbone_scale=1.0,
): ):
## Round steps up to nearest multiple of output_period, plus 1 ## Round steps up to nearest multiple of output_period, plus 1
if minimization_steps > 0:
raise NotImplementedError
minimization_steps = ((minimization_steps+minimization_output_period-1)//minimization_output_period)*minimization_output_period+1
coarse_steps = ((coarse_steps+coarse_output_period-1)//coarse_output_period)*coarse_output_period+1 coarse_steps = ((coarse_steps+coarse_output_period-1)//coarse_output_period)*coarse_output_period+1
fine_steps = ((fine_steps+fine_output_period-1)//fine_output_period) fine_steps = ((fine_steps+fine_output_period-1)//fine_output_period)
if fine_steps == 1: fine_steps += 1 if fine_steps == 1: fine_steps += 1
fine_steps = fine_steps*fine_output_period+1 fine_steps = fine_steps*fine_output_period+1
ret = None ret = None
d_orig = os.getcwd() d_orig = os.getcwd()
try: try:
...@@ -38,89 +48,88 @@ def multiresolution_simulation( model, output_name, ...@@ -38,89 +48,88 @@ def multiresolution_simulation( model, output_name,
os.chdir(directory) os.chdir(directory)
output_directory = "output" output_directory = "output"
simulation_step = 0
def run_step(num_steps, simargs, do_coordinate_average=False):
""" Function runs one step of the simulation protocol process """
nonlocal simulation_step
output_prefix = "{}-{}".format(output_name, simulation_step)
full_output_prefix = "{}/{}".format(output_directory,output_prefix)
model.simulate( output_name = output_prefix, num_steps = num_steps, **simargs )
if do_coordinate_average:
try:
coordinates = readAvgArbdCoords('%s.psf' % output_prefix,'%s.pdb' % output_prefix, '%s.dcd' % full_output_prefix, rmsdThreshold=1)
except:
coordinates = readAvgArbdCoords('%s.psf' % output_prefix,'%s.pdb' % output_prefix, '%s.0.dcd' % full_output_prefix, rmsdThreshold=1)
else:
try:
coordinates = readArbdCoords('%s.restart' % full_output_prefix)
except:
coordinates = readArbdCoords('%s.0.restart' % full_output_prefix)
model.update_splines(coordinates)
simulation_step += 1
coarse_model_args = dict( max_basepairs_per_bead = 5,
max_nucleotides_per_bead = 5,
local_twist = coarse_local_twist,
escapable_twist = True )
# TODO: add the output directory in to the readArbdCoords functions or make it an attribute of the model object # TODO: add the output directory in to the readArbdCoords functions or make it an attribute of the model object
""" Coarse simulation """ """ Prepare coarse model for minimization and coarse simulation """
simargs = dict(timestep=200e-6, output_period=coarse_output_period, gpu=gpu) if remove_long_bonds:
raise NotImplementedError("TODO: remove long bonds")
model.clear_beads()
model.generate_bead_model( **coarse_model_args )
model._clear_beads() """ Minimization """
model._generate_bead_model( 5, 5, local_twist=False ) if minimization_steps > 0:
simargs = dict(timestep=200e-6, output_period=minimization_output_period, gpu=gpu)
run_step(num_steps=minimization_steps, simargs=simargs)
model.clear_beads()
model.generate_bead_model( **coarse_model_args )
""" Coarse simulation """
simargs = dict(timestep=200e-6, output_period=coarse_output_period, gpu=gpu)
if remove_long_bonds: if remove_long_bonds:
output_prefix = "%s-0" % output_name run_step(num_steps=0.05*coarse_steps, simargs=simargs)
full_output_prefix = "%s/%s" % (output_directory,output_prefix) model.clear_beads()
## TODO Remove long bonds model.generate_bead_model( **coarse_model_args )
model.simulate( output_name = output_prefix, numSteps=0.05*coarse_steps, **simargs ) run_step(num_steps=0.95*coarse_steps, simargs=simargs)
try:
coordinates = readArbdCoords('%s.restart' % full_output_prefix)
except:
coordinates = readArbdCoords('%s.0.restart' % full_output_prefix)
output_prefix = "%s-1" % output_name
model.update_splines(coordinates)
model.simulate( output_prefix = output_prefix, num_steps=0.95*coarse_steps, **simargs )
else: else:
output_prefix = "%s-1" % output_name run_step(num_steps=coarse_steps, simargs=simargs)
full_output_prefix = "%s/%s" % (output_directory,output_prefix)
model.simulate( output_name = output_prefix, num_steps=coarse_steps, **simargs )
try:
coordinates = readArbdCoords('%s.restart' % full_output_prefix)
except:
coordinates = readArbdCoords('%s.0.restart' % full_output_prefix)
""" Fine simulation """ """ Fine simulation """
output_prefix = "%s-2" % output_name simargs = dict(timestep=50e-6, output_period=fine_output_period, gpu=gpu)
full_output_prefix = "%s/%s" % (output_directory,output_prefix) model.clear_beads()
simargs['timestep'] = 50e-6 model.generate_bead_model( 1, 1, local_twist=True, escapable_twist=True )
simargs['output_period'] = fine_output_period run_step(num_steps=fine_steps, simargs=simargs, do_coordinate_average=(fine_steps > 2*fine_output_period+1))
model.update_splines(coordinates)
model._clear_beads()
model._generate_bead_model( 1, 1, local_twist=True, escapable_twist=True )
model.simulate( output_name = output_prefix, num_steps=fine_steps, **simargs )
if fine_steps <= 2*fine_output_period+1:
try:
coordinates = readArbdCoords('%s.restart' % full_output_prefix)
except:
coordinates = readArbdCoords('%s.0.restart' % full_output_prefix)
else:
try:
coordinates = readAvgArbdCoords('%s.psf' % output_prefix,'%s.pdb' % output_prefix, '%s.dcd' % full_output_prefix, rmsdThreshold=1)
except:
coordinates = readAvgArbdCoords('%s.psf' % output_prefix,'%s.pdb' % output_prefix, '%s.0.dcd' % full_output_prefix, rmsdThreshold=1)
""" Freeze twist """ """ Freeze twist """
output_prefix = "%s-3" % output_name model.clear_beads()
full_output_prefix = "%s/%s" % (output_directory,output_prefix) model.generate_bead_model( 1, 1, local_twist=True, escapable_twist=False )
model.update_splines(coordinates) run_step(num_steps=fine_steps, simargs=simargs, do_coordinate_average=(fine_steps > 2*fine_output_period+1))
model._clear_beads()
model._generate_bead_model( 1, 1, local_twist=True, escapable_twist=False )
model.simulate( output_name = output_prefix, num_steps=fine_steps, **simargs )
if fine_steps <= 2*fine_output_period+1:
try:
coordinates = readArbdCoords('%s.restart' % full_output_prefix)
except:
coordinates = readArbdCoords('%s.0.restart' % full_output_prefix)
else:
try:
coordinates = readAvgArbdCoords('%s.psf' % output_prefix,'%s.pdb' % output_prefix, '%s.dcd' % full_output_prefix, rmsdThreshold=1)
except:
coordinates = readAvgArbdCoords('%s.psf' % output_prefix,'%s.pdb' % output_prefix, '%s.0.dcd' % full_output_prefix, rmsdThreshold=1)
""" Atomic simulation """ """ Atomic simulation """
output_prefix = "%s-4" % output_name model.clear_beads()
full_output_prefix = "%s/%s" % (output_directory,output_prefix) model.generate_atomic_model(scale=backbone_scale)
model.update_splines(coordinates)
model._clear_beads() output_prefix = "{}-{}".format(output_name, simulation_step)
model._generate_atomic_model(scale=backbone_scale) # full_output_prefix = "%s/%s" % (output_directory,output_prefix)
model.write_atomic_ENM( output_prefix )
model.atomic_simulate( output_name = output_prefix )
try: try:
shutil.copytree( get_resource_path("charmm36.nbfix"), "charmm36.nbfix" ) shutil.copytree( get_resource_path("charmm36.nbfix"), "charmm36.nbfix" )
except FileExistsError: except FileExistsError:
... ...
model.write_atomic_ENM( output_prefix )
model.atomic_simulate( output_name = output_prefix )
ret = directory ret = directory
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment