From f9d7ee2b3adc4c3e758a60abfffa7cb826c182fe Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Thu, 2 Jan 2020 12:31:17 -0600
Subject: [PATCH] Optionally run enrg-md simulations
---
bin/enrgmd | 2 +-
bin/mrdna | 11 +++++++---
mrdna/model/arbdmodel.py | 44 +++++++++++++++++++++++++++++++++++++++-
mrdna/simulate.py | 6 ++++--
4 files changed, 56 insertions(+), 7 deletions(-)
diff --git a/bin/enrgmd b/bin/enrgmd
index 25d9959..ed11a17 100755
--- a/bin/enrgmd
+++ b/bin/enrgmd
@@ -78,7 +78,7 @@ http://dx.doi.org/10.1093/nar/gkw155
os.makedirs('output')
except FileExistsError:
...
- model.atomic_simulate( output_name = prefix )
+ model.atomic_simulate( output_name = prefix, dry_run=True )
except:
raise
diff --git a/bin/mrdna b/bin/mrdna
index f539741..06fd281 100755
--- a/bin/mrdna
+++ b/bin/mrdna
@@ -57,6 +57,10 @@ parser.add_argument('--oxdna-output-period', type=float, default=1e4,
parser.add_argument('--backbone-scale', type=float, default=1.0,
help='Factor to scale DNA backbone in atomic model; try 0.25 to avoid clashes for atomistic simulations')
+
+parser.add_argument('--run-enrg-md', action='store_true',
+ help='Perform the ENRG-MD simulation?')
+
parser.add_argument('--debug', action='store_true',
help='Run through the python debugger?')
@@ -128,7 +132,7 @@ def main():
model._clear_beads()
model._generate_atomic_model(scale=args.backbone_scale)
model.write_atomic_ENM( prefix )
- model.atomic_simulate( output_name = prefix )
+ model.atomic_simulate( output_name = prefix, dry_run=True )
elif args.draw_tubes is True:
output_name = prefix + ".tubes.tcl"
model.vmd_tube_tcl( output_name )
@@ -140,7 +144,7 @@ def main():
model._clear_beads()
model._generate_atomic_model(scale=args.backbone_scale)
model.write_atomic_ENM( prefix )
- model.atomic_simulate( output_name = prefix )
+ model.atomic_simulate( output_name = prefix, dry_run=True )
else:
run_args = dict(
model = model,
@@ -158,7 +162,8 @@ def main():
fine_steps = int(args.fine_steps),
backbone_scale = args.backbone_scale,
oxdna_steps = args.oxdna_steps,
- oxdna_output_period = args.oxdna_output_period
+ oxdna_output_period = args.oxdna_output_period,
+ run_enrg_md = args.run_enrg_md
)
simulate( **run_args )
diff --git a/mrdna/model/arbdmodel.py b/mrdna/model/arbdmodel.py
index dd173d2..0a35826 100644
--- a/mrdna/model/arbdmodel.py
+++ b/mrdna/model/arbdmodel.py
@@ -1187,7 +1187,7 @@ if {{$nLast == 0}} {{
run {num_steps:d}
""".format(**format_data))
- def atomic_simulate(self, output_name, output_directory='output'):
+ def atomic_simulate(self, output_name, output_directory='output', dry_run = False, namd2=None, log_file=None, num_procs=None, gpu=None):
if self.cacheUpToDate == False: # TODO: remove cache?
self._countParticleTypes()
self._updateParticleOrder()
@@ -1199,6 +1199,48 @@ run {num_steps:d}
self.write_namd_configuration( output_name, output_directory = output_directory )
os.sync()
+ if not dry_run:
+ if namd2 is None:
+ for path in os.environ["PATH"].split(os.pathsep):
+ path = path.strip('"')
+ fname = os.path.join(path, "namd2")
+ if os.path.isfile(fname) and os.access(fname, os.X_OK):
+ namd2 = fname
+ break
+
+ if namd2 is None: raise Exception("NAMD2 was not found")
+
+ if not os.path.exists(namd2):
+ raise Exception("NAMD2 was not found")
+ if not os.path.isfile(namd2):
+ raise Exception("NAMD2 was not found")
+ if not os.access(namd2, os.X_OK):
+ raise Exception("NAMD2 is not executable")
+
+ if not os.path.exists(output_directory):
+ os.makedirs(output_directory)
+ elif not os.path.isdir(output_directory):
+ raise Exception("output_directory '%s' is not a directory!" % output_directory)
+
+ if num_procs is None:
+ import multiprocessing
+ num_procs = max(1,multiprocessing.cpu_count()-1)
+
+ cmd = [namd2, '+p{}'.format(num_procs), "%s.namd" % output_name]
+ cmd = tuple(str(x) for x in cmd)
+
+ print("Running NAMD2 with: %s" % " ".join(cmd))
+ if log_file is None or (hasattr(log_file,'write') and callable(log_file.write)):
+ fd = sys.stdout if log_file is None else log_file
+ process = subprocess.Popen(cmd, stdout=subprocess.PIPE, universal_newlines=True)
+ for line in process.stdout:
+ fd.write(line)
+ fd.flush()
+ else:
+ with open(log_file,'w') as fd:
+ process = subprocess.Popen(cmd, stdout=log_file, universal_newlines=True)
+ process.communicate()
+
""" oxDNA """
## https://dna.physics.ox.ac.uk/index.php/Documentation#Input_file
diff --git a/mrdna/simulate.py b/mrdna/simulate.py
index 348c452..e8aa7ea 100644
--- a/mrdna/simulate.py
+++ b/mrdna/simulate.py
@@ -65,6 +65,7 @@ def multiresolution_simulation( model, output_name,
backbone_scale=1.0,
oxdna_steps = None,
oxdna_output_period = None,
+ run_enrg_md = False
):
## Round steps up to nearest multiple of output_period, plus 1
@@ -171,13 +172,14 @@ def multiresolution_simulation( model, output_name,
# full_output_prefix = "%s/%s" % (output_directory,output_prefix)
model.write_atomic_ENM( output_prefix )
- model.atomic_simulate( output_name = output_prefix )
-
try:
shutil.copytree( get_resource_path("charmm36.nbfix"), "charmm36.nbfix" )
except FileExistsError:
...
+ model.atomic_simulate( output_name = output_prefix, dry_run = not run_enrg_md )
+
+
ret = directory
--
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