def write(self, inputdir, outputdir):
""" Write the equilibration protocol
Writes the equilibration protocol and files into a folder for execution
using files inside the inputdir directory
Parameters
----------
inputdir : str
Path to a directory containing the files produced by a build process.
outputdir : str
Directory where to write the equilibration setup files.
Examples
--------
>>> md = Equilibration()
>>> md.write('./build','./equil')
"""
self._findFiles(inputdir)
self._amberFixes()
from htmd.units import convert
numsteps = convert(self.timeunits,
'timesteps',
self.runtime,
timestep=self.acemd.timestep)
self.acemd.temperature = self.temperature
self.acemd.thermostattemp = self.temperature
self.acemd.run = str(numsteps)
if self.constraintsteps is None:
constrsteps = int(numsteps / 2)
else:
constrsteps = int(self.constraintsteps)
# Adding the default restraints of the equilibration
restraints = list()
restraints.append(
AtomRestraint('protein and noh and not name CA', 0,
[(0.1, 0), (0, constrsteps)]))
restraints.append(
AtomRestraint('protein and name CA', 0, [(1, 0),
(0, constrsteps)]))
if self.restraints is not None:
restraints += self.restraints
self.acemd.restraints = restraints
if self.acemd.celldimension is None and self.acemd.extendedsystem is None:
inmol = Molecule(os.path.join(inputdir, self.acemd.coordinates))
coords = inmol.get('coords', sel='water')
if coords.size == 0: # It's a vacuum simulation
coords = inmol.get('coords', sel='all')
dim = np.max(coords, axis=0) - np.min(coords, axis=0)
dim = dim + 12.
else:
dim = np.max(coords, axis=0) - np.min(coords, axis=0)
self.acemd.celldimension = '{} {} {}'.format(
dim[0], dim[1], dim[2])
if self.useconstantratio:
self.acemd.useconstantratio = 'on'
self.acemd.setup(inputdir, outputdir, overwrite=True)
# Compare with reference
refdir = home(dataDir=os.path.join('test-equilibration', pdbid, 'prerun'))
files = [os.path.basename(f) for f in glob(os.path.join(refdir, '*'))]
match, mismatch, error = filecmp.cmpfiles(refdir,
tmpdir,
files,
shallow=False)
if len(mismatch) != 0 or len(error) != 0 or len(match) != len(files):
raise RuntimeError(
'Different results produced by Equilibration.write for '
'test {} between {} and {} in files {}.'.format(
pdbid, refdir, tmpdir, mismatch))
# from htmd.protocols.production_v5 import ProductionAcemd3, GroupRestraint, AtomRestraint
r = list()
r.append(
GroupRestraint('segid P2',
5, [(10, '10ns'), (5, '15ns'), (0, '20ns')],
axes='z'))
r.append(
AtomRestraint('segid P1 and name CA', 0.1, [(10, '10ns'), (5, '15ns'),
(0, '20ns')]))
eq = EquilibrationAcemd3()
eq.runtime = 4
eq.timeunits = 'ns'
eq.temperature = 300
eq.restraints = r
# eq.write('/workspace5/pablo/bound_KIX_cMYB/1_build/2-struct/', '/tmp/testdir2/')