def setup_md(self, struct=None, top=None):
"""
setup an equilibration md run using the contents of the universe, but do not actually run it.
@return an MDManager object loaded with the trr to run an equilibration.
"""
logging.debug("struct = {}, top = {}".format(struct, top ))
if struct is None or top is None:
struct = self.universe
top = self.top
logging.info("setting up md for self.universe")
else:
logging.info("setting up md for solvated struct, top")
md_args = self.md_args
md_args['ref_t'] = self.config[TEMPERATURE]
md_args['gen-temp'] = self.config[TEMPERATURE]
return md.setup_md(struct=struct, \
top=top, \
top_includes=self.top_includes, \
nsteps=self.config[MD_STEPS], \
multi=self.config[MULTI], \
deffnm="md", \
mainselection=self.mainselection, \
**md_args)
def setup_equilibrate(self, struct=None, top=None):
"""
setup an equilibration md run using the contents of the universe, but do not actually run it.
@return an MDManager object loaded with the trr to run an equilibration.
"""
if struct is None or top is None:
struct = self.universe
top = self.top
logging.info("setting up equilibration for self.universe")
else:
logging.info("setting up equilibration for solvated struct, top")
eq_args = self.eq_args
eq_args['ref_t'] = self.config[TEMPERATURE]
eq_args['gen-temp'] = self.config[TEMPERATURE]
return md.setup_md(struct=struct, \
top=top, \
top_includes=self.top_includes, \
nsteps=self.config[EQ_STEPS], \
deffnm="eq", \
mainselection=self.mainselection, \
**eq_args)
def setup_equilibriate(self, struct=None, top=None):
"""
setup an equilibriation md run using the contents of the universe, but do not actually run it.
@return an MDManager object loaded with the trr to run an equilibriation.
"""
if struct is None or top is None:
struct = self.universe
top = self.top
logging.info("setting up equilibriation for self.universe")
else:
logging.info("setting up equilibriation for solvated struct, top")
return md.setup_md(struct=struct, \
top=top, \
top_includes=self.top_includes, \
nsteps=self.config[EQ_STEPS], \
deffnm="eq", \
mainselection=self.mainselection, \
**self.eq_args)
def setup_md(self, struct=None, top=None):
"""
setup an equilibriation md run using the contents of the universe, but do not actually run it.
@return an MDManager object loaded with the trr to run an equilibriation.
"""
logging.debug("struct = {}, top = {}".format(struct, top))
if struct is None or top is None:
struct = self.universe
top = self.top
logging.info("setting up md for self.universe")
else:
logging.info("setting up md for solvated struct, top")
return md.setup_md(struct=struct, \
top=top, \
top_includes=self.top_includes, \
nsteps=self.config[MD_STEPS], \
multi=self.config[MULTI], \
deffnm="md", \
mainselection=self.mainselection, \
**self.md_args)