def energy_minimize(dirname='em', mdp=config.templates['em.mdp'],
struct='solvate/ionized.pdb', top='top/system.top',
output='em.pdb', deffnm="em",
mdrunner=None, **kwargs):
"""Energy minimize the system.
This sets up the system (creates run input files) and also runs
``mdrun_d``. Thus it can take a while.
Additional itp files should be in the same directory as the top file.
Many of the keyword arguments below already have sensible values.
:Keywords:
*dirname*
set up under directory dirname [em]
*struct*
input structure (gro, pdb, ...) [solvate/ionized.pdb]
*output*
output structure (will be put under dirname) [em.pdb]
*deffnm*
default name for mdrun-related files [em]
*top*
topology file [top/system.top]
*mdp*
mdp file (or use the template) [templates/em.mdp]
*includes*
additional directories to search for itp files
*mdrunner*
:class:`gromacs.run.MDrunner` class; by defauly we
just try :func:`gromacs.mdrun_d` and :func:`gromacs.mdrun` but a
MDrunner class gives the user the ability to run mpi jobs
etc. [None]
*kwargs*
remaining key/value pairs that should be changed in the
template mdp file, eg ``nstxtcout=250, nstfout=250``.
.. note:: If :func:`~gromacs.mdrun_d` is not found, the function
falls back to :func:`~gromacs.mdrun` instead.
"""
structure = realpath(struct)
topology = realpath(top)
mdp_template = config.get_template(mdp)
deffnm = deffnm.strip()
# write the processed topology to the default output
kwargs.setdefault('pp', 'processed.top')
# filter some kwargs that might come through when feeding output
# from previous stages such as solvate(); necessary because *all*
# **kwargs must be *either* substitutions in the mdp file *or* valid
# command line parameters for ``grompp``.
kwargs.pop('ndx', None)
# mainselection is not used but only passed through; right now we
# set it to the default that is being used in all argument lists
# but that is not pretty. TODO.
mainselection = kwargs.pop('mainselection', '"Protein"')
# only interesting when passed from solvate()
qtot = kwargs.pop('qtot', 0)
mdp = deffnm+'.mdp'
tpr = deffnm+'.tpr'
logger.info("[%(dirname)s] Energy minimization of struct=%(struct)r, top=%(top)r, mdp=%(mdp)r ..." % vars())
add_mdp_includes(topology, kwargs)
if qtot != 0:
# At the moment this is purely user-reported and really only here because
# it might get fed into the function when using the keyword-expansion pipeline
# usage paradigm.
wmsg = "Total charge was reported as qtot = %(qtot)g <> 0; probably a problem." % vars()
logger.warn(wmsg)
warnings.warn(wmsg, category=BadParameterWarning)
with in_dir(dirname):
unprocessed = gromacs.cbook.edit_mdp(mdp_template, new_mdp=mdp, **kwargs)
check_mdpargs(unprocessed)
gromacs.grompp(f=mdp, o=tpr, c=structure, p=topology, **unprocessed)
mdrun_args = dict(v=True, stepout=10, deffnm=deffnm, c=output)
if mdrunner is None:
try:
gromacs.mdrun_d(**mdrun_args)
except (AttributeError, OSError):
# fall back to mdrun if no double precision binary
wmsg = "No 'mdrun_d' binary found so trying 'mdrun' instead.\n"\
"(Note that energy minimization runs better with mdrun_d.)"
logger.warn(wmsg)
warnings.warn(wmsg, category=AutoCorrectionWarning)
gromacs.mdrun(**mdrun_args)
else:
# user wants full control and provides simulation.MDrunner **class**
# NO CHECKING --- in principle user can supply any callback they like
mdrun = mdrunner(**mdrun_args)
mdrun.run()
# em.gro --> gives 'Bad box in file em.gro' warning --- why??
# --> use em.pdb instead.
if not os.path.exists(output):
errmsg = "Energy minimized system NOT produced."
logger.error(errmsg)
raise GromacsError(errmsg)
final_struct = realpath(output)
logger.info("[%(dirname)s] energy minimized structure %(final_struct)r" % vars())
return {'struct': final_struct,
'top': topology,
'mainselection': mainselection,
}
def _setup_MD(dirname,
deffnm='md', mdp=config.templates['md_OPLSAA.mdp'],
struct=None,
top='top/system.top', ndx=None,
mainselection='"Protein"',
qscript=config.qscript_template, qname=None, startdir=None, mdrun_opts="", budget=None, walltime=1/3.,
dt=0.002, runtime=1e3, multi=1, **mdp_kwargs):
"""Generic function to set up a ``mdrun`` MD simulation.
See the user functions for usage.
@param qname: name of the queing system, may be None.
@param multi: setup multiple concurrent simulations. These are based upon deffnm being set,
and a set of mdp / tpr are created named [deffnm]0.tpr. [deffnm]1.tpr, ...
"""
if struct is None:
raise ValueError('struct must be set to a input structure')
structure = realpath(struct)
topology = realpath(top)
try:
index = realpath(ndx)
except AttributeError: # (that's what realpath(None) throws...)
index = None # None is handled fine below
qname = mdp_kwargs.pop('sgename', qname) # compatibility for old scripts
qscript = mdp_kwargs.pop('sge', qscript) # compatibility for old scripts
qscript_template = config.get_template(qscript)
mdp_template = config.get_template(mdp)
nsteps = int(float(runtime)/float(dt))
mainindex = deffnm + '.ndx'
final_structure = deffnm + '.pdb' # guess... really depends on templates,could also be DEFFNM.pdb
# write the processed topology to the default output
mdp_parameters = {'nsteps':nsteps, 'dt':dt}
mdp_parameters.update(mdp_kwargs)
add_mdp_includes(topology, mdp_parameters)
# the basic result dictionary
# depending on options, various bits might be added to this.
result = {'struct': realpath(os.path.join(dirname, final_structure)), # guess
'top': topology,
'ndx': index, # possibly mainindex
'mainselection': mainselection,
'deffnm': deffnm, # return deffnm (tpr = deffnm.tpr!)
}
with in_dir(dirname):
if not (mdp_parameters.get('Tcoupl','').lower() == 'no' or mainselection is None):
logger.info("[%(dirname)s] Automatic adjustment of T-coupling groups" % vars())
# make index file in almost all cases; with mainselection == None the user
# takes FULL control and also has to provide the template or index
groups = make_main_index(structure, selection=mainselection,
oldndx=index, ndx=mainindex)
natoms = dict([(g['name'], float(g['natoms'])) for g in groups])
tc_group_names = ('__main__', '__environment__') # defined in make_main_index()
try:
x = natoms['__main__']/natoms['__environment__']
except KeyError:
x = 0 # force using SYSTEM in code below
wmsg = "Missing __main__ and/or __environment__ index group.\n" \
"This probably means that you have an atypical system. You can " \
"set mainselection=None and provide your own mdp and index files " \
"in order to set up temperature coupling.\n" \
"If no T-coupling is required then set Tcoupl='no'.\n" \
"For now we will just couple everything to 'System'."
logger.warn(wmsg)
warnings.warn(wmsg, category=AutoCorrectionWarning)
if x < 0.1:
# couple everything together
tau_t = firstof(mdp_parameters.pop('tau_t', 0.1))
ref_t = firstof(mdp_parameters.pop('ref_t', 300))
# combine all in one T-coupling group
mdp_parameters['tc-grps'] = 'System'
mdp_parameters['tau_t'] = tau_t # this overrides the commandline!
mdp_parameters['ref_t'] = ref_t # this overrides the commandline!
mdp_parameters['gen-temp'] = mdp_parameters.pop('gen_temp', ref_t)
wmsg = "Size of __main__ is only %.1f%% of __environment__ so " \
"we use 'System' for T-coupling and ref_t = %g K and " \
"tau_t = %g 1/ps (can be changed in mdp_parameters).\n" \
% (x * 100, ref_t, tau_t)
logger.warn(wmsg)
warnings.warn(wmsg, category=AutoCorrectionWarning)
else:
# couple protein and bath separately
n_tc_groups = len(tc_group_names)
tau_t = asiterable(mdp_parameters.pop('tau_t', 0.1))
ref_t = asiterable(mdp_parameters.pop('ref_t', 300))
if len(tau_t) != n_tc_groups:
tau_t = n_tc_groups * [tau_t[0]]
wmsg = "%d coupling constants should have been supplied for tau_t. "\
"Using %f 1/ps for all of them." % (n_tc_groups, tau_t[0])
logger.warn(wmsg)
warnings.warn(wmsg, category=AutoCorrectionWarning)
if len(ref_t) != n_tc_groups:
ref_t = n_tc_groups * [ref_t[0]]
wmsg = "%d temperatures should have been supplied for ref_t. "\
"Using %g K for all of them." % (n_tc_groups, ref_t[0])
logger.warn(wmsg)
warnings.warn(wmsg, category=AutoCorrectionWarning)
mdp_parameters['tc-grps'] = tc_group_names
mdp_parameters['tau_t'] = tau_t
mdp_parameters['ref_t'] = ref_t
mdp_parameters['gen-temp'] = mdp_parameters.pop('gen_temp', ref_t[0])
index = realpath(mainindex)
if mdp_parameters.get('Tcoupl','').lower() == 'no':
logger.info("Tcoupl == no: disabling all temperature coupling mdp options")
mdp_parameters['tc-grps'] = ""
mdp_parameters['tau_t'] = ""
mdp_parameters['ref_t'] = ""
mdp_parameters['gen-temp'] = ""
if mdp_parameters.get('Pcoupl','').lower() == 'no':
logger.info("Pcoupl == no: disabling all pressure coupling mdp options")
mdp_parameters['tau_p'] = ""
mdp_parameters['ref_p'] = ""
mdp_parameters['compressibility'] = ""
# do multiple concurrent simulations - ensemble sampling
if multi > 1:
for i in range(multi):
new_mdp = deffnm + str(i) + ".mdp"
mdout = deffnm + "out" + str(i) + ".mdp"
pp = "processed" + str(i) + ".top"
tpr = deffnm + str(i) + ".tpr"
# doing ensemble sampling, so give differnt seeds for each one
# if we are using 32 bit gromacs, make seeds are are 32 bit even on
# 64 bit machine
mdp_parameters["andersen_seed"] = random.randint(0,2**31)
mdp_parameters["gen_seed"] = random.randint(0,2**31)
mdp_parameters["ld_seed"] = random.randint(0,2**31)
unprocessed = gromacs.cbook.edit_mdp(mdp_template, new_mdp=new_mdp, **mdp_parameters)
check_mdpargs(unprocessed)
gromacs.grompp(f=new_mdp, p=topology, c=structure, n=index, o=tpr,
po=mdout, pp=pp, **unprocessed)
# only add multi to result if we really are doing multiple runs
result["multi"] = multi
else:
new_mdp = deffnm + '.mdp'
tpr = deffnm + '.tpr'
unprocessed = gromacs.cbook.edit_mdp(mdp_template, new_mdp=new_mdp, **mdp_parameters)
check_mdpargs(unprocessed)
gromacs.grompp(f=new_mdp, p=topology, c=structure, n=index, o=tpr,
po="mdout.mdp", pp="processed.top", **unprocessed)
# generate scripts for queing system if requested
if qname is not None:
runscripts = gromacs.qsub.generate_submit_scripts(
qscript_template, deffnm=deffnm, jobname=qname, budget=budget,
startdir=startdir, mdrun_opts=mdrun_opts, walltime=walltime)
result["qscript"] =runscripts
logger.info("[%(dirname)s] All files set up for a run time of %(runtime)g ps "
"(dt=%(dt)g, nsteps=%(nsteps)g)" % vars())
result.update(mdp_kwargs) # return extra mdp args so that one can use them for prod run
result.pop('define', None) # but make sure that -DPOSRES does not stay...
return result
def _setup_MD(
dirname,
deffnm="md",
mdp=config.templates["md_OPLSAA.mdp"],
struct=None,
top="top/system.top",
ndx=None,
mainselection='"Protein"',
qscript=config.qscript_template,
qname=None,
startdir=None,
mdrun_opts="",
budget=None,
walltime=1 / 3.0,
dt=0.002,
runtime=1e3,
**mdp_kwargs
):
"""Generic function to set up a ``mdrun`` MD simulation.
See the user functions for usage.
"""
if struct is None:
raise ValueError("struct must be set to a input structure")
structure = realpath(struct)
topology = realpath(top)
try:
index = realpath(ndx)
except AttributeError: # (that's what realpath(None) throws...)
index = None # None is handled fine below
qname = mdp_kwargs.pop("sgename", qname) # compatibility for old scripts
qscript = mdp_kwargs.pop("sge", qscript) # compatibility for old scripts
qscript_template = config.get_template(qscript)
mdp_template = config.get_template(mdp)
nsteps = int(float(runtime) / float(dt))
mdp = deffnm + ".mdp"
tpr = deffnm + ".tpr"
mainindex = deffnm + ".ndx"
final_structure = deffnm + ".gro" # guess... really depends on templates,could also be DEFFNM.pdb
# write the processed topology to the default output
mdp_parameters = {"nsteps": nsteps, "dt": dt, "pp": "processed.top"}
mdp_parameters.update(mdp_kwargs)
add_mdp_includes(topology, mdp_parameters)
logger.info("[%(dirname)s] input mdp = %(mdp_template)r", vars())
with in_dir(dirname):
if not (mdp_parameters.get("Tcoupl", "").lower() == "no" or mainselection is None):
logger.info("[%(dirname)s] Automatic adjustment of T-coupling groups" % vars())
# make index file in almost all cases; with mainselection == None the user
# takes FULL control and also has to provide the template or index
groups = make_main_index(structure, selection=mainselection, oldndx=index, ndx=mainindex)
natoms = dict([(g["name"], float(g["natoms"])) for g in groups])
tc_group_names = ("__main__", "__environment__") # defined in make_main_index()
try:
x = natoms["__main__"] / natoms["__environment__"]
except KeyError:
x = 0 # force using SYSTEM in code below
wmsg = (
"Missing __main__ and/or __environment__ index group.\n"
"This probably means that you have an atypical system. You can "
"set mainselection=None and provide your own mdp and index files "
"in order to set up temperature coupling.\n"
"If no T-coupling is required then set Tcoupl='no'.\n"
"For now we will just couple everything to 'System'."
)
logger.warn(wmsg)
warnings.warn(wmsg, category=AutoCorrectionWarning)
if x < 0.1:
# couple everything together
tau_t = firstof(mdp_parameters.pop("tau_t", 0.1))
ref_t = firstof(mdp_parameters.pop("ref_t", 300))
# combine all in one T-coupling group
mdp_parameters["tc-grps"] = "System"
mdp_parameters["tau_t"] = tau_t # this overrides the commandline!
mdp_parameters["ref_t"] = ref_t # this overrides the commandline!
mdp_parameters["gen-temp"] = mdp_parameters.pop("gen_temp", ref_t)
wmsg = (
"Size of __main__ is only %.1f%% of __environment__ so "
"we use 'System' for T-coupling and ref_t = %g K and "
"tau_t = %g 1/ps (can be changed in mdp_parameters).\n" % (x * 100, ref_t, tau_t)
)
logger.warn(wmsg)
warnings.warn(wmsg, category=AutoCorrectionWarning)
else:
# couple protein and bath separately
n_tc_groups = len(tc_group_names)
tau_t = asiterable(mdp_parameters.pop("tau_t", 0.1))
ref_t = asiterable(mdp_parameters.pop("ref_t", 300))
if len(tau_t) != n_tc_groups:
tau_t = n_tc_groups * [tau_t[0]]
wmsg = (
"%d coupling constants should have been supplied for tau_t. "
"Using %f 1/ps for all of them." % (n_tc_groups, tau_t[0])
)
logger.warn(wmsg)
warnings.warn(wmsg, category=AutoCorrectionWarning)
if len(ref_t) != n_tc_groups:
ref_t = n_tc_groups * [ref_t[0]]
wmsg = "%d temperatures should have been supplied for ref_t. " "Using %g K for all of them." % (
n_tc_groups,
ref_t[0],
)
logger.warn(wmsg)
warnings.warn(wmsg, category=AutoCorrectionWarning)
mdp_parameters["tc-grps"] = tc_group_names
mdp_parameters["tau_t"] = tau_t
mdp_parameters["ref_t"] = ref_t
mdp_parameters["gen-temp"] = mdp_parameters.pop("gen_temp", ref_t[0])
index = realpath(mainindex)
if mdp_parameters.get("Tcoupl", "").lower() == "no":
logger.info("Tcoupl == no: disabling all temperature coupling mdp options")
mdp_parameters["tc-grps"] = ""
mdp_parameters["tau_t"] = ""
mdp_parameters["ref_t"] = ""
mdp_parameters["gen-temp"] = ""
if mdp_parameters.get("Pcoupl", "").lower() == "no":
logger.info("Pcoupl == no: disabling all pressure coupling mdp options")
mdp_parameters["tau_p"] = ""
mdp_parameters["ref_p"] = ""
mdp_parameters["compressibility"] = ""
unprocessed = gromacs.cbook.edit_mdp(mdp_template, new_mdp=mdp, **mdp_parameters)
check_mdpargs(unprocessed)
gromacs.grompp(f=mdp, p=topology, c=structure, n=index, o=tpr, **unprocessed)
runscripts = gromacs.qsub.generate_submit_scripts(
qscript_template,
deffnm=deffnm,
jobname=qname,
budget=budget,
startdir=startdir,
mdrun_opts=mdrun_opts,
walltime=walltime,
)
logger.info("[%(dirname)s] output mdp = %(mdp)r", vars())
logger.info("[%(dirname)s] output ndx = %(ndx)r", vars())
logger.info("[%(dirname)s] output tpr = %(tpr)r", vars())
logger.info("[%(dirname)s] output runscripts = %(runscripts)r", vars())
logger.info(
"[%(dirname)s] All files set up for a run time of %(runtime)g ps " "(dt=%(dt)g, nsteps=%(nsteps)g)" % vars()
)
kwargs = {
"struct": realpath(os.path.join(dirname, final_structure)), # guess
"top": topology,
"ndx": index, # possibly mainindex
"qscript": runscripts,
"mainselection": mainselection,
"deffnm": deffnm, # return deffnm (tpr = deffnm.tpr!)
}
kwargs.update(mdp_kwargs) # return extra mdp args so that one can use them for prod run
return kwargs