def minimize_liq(self, in_gromos_simulation_system: Gromos_System, prev_JobID: int):
"""
Minimize Liquide
Parameters
----------
in_gromos_simulation_system : Gromos_System
input Gromos System to minimize
prev_JobID
previous jobID to wait for
Returns
-------
emin_sys : Gromos_System
Energy minimized Gromos System
jobID : int
ID of submitted job for the next job to wait for (only relevant for LSF)
"""
in_gromos_simulation_system.adapt_imd_automatically = False
in_gromos_simulation_system.imd = self.imd_liq_min
emin_sys = simulation(
in_gromos_simulation_system=in_gromos_simulation_system,
override_project_dir=self.groSys_liq.work_folder,
step_name=self.system_name + "_emin",
submission_system=self._subsystem,
analysis_script=simulation_analysis.do,
verbose=self.verbose,
)
return emin_sys, emin_sys._last_jobID
def sd(
in_gromos_system: Gromos_System,
step_name: str = "sd",
override_project_dir: str = None,
in_imd_path=None,
submission_system: _SubmissionSystem = LOCAL(),
simulation_runs: int = 1,
equilibration_runs: int = 0,
initialize_first_run=False,
previous_simulation_run: int = None,
_template_imd_path: str = template_sd,
_no_double_submit_check: bool = False,
analysis_script: callable = simulation_analysis.do,
verbose: bool = True,
) -> Tuple[Gromos_System, int]:
return simulation(
in_gromos_simulation_system=in_gromos_system,
override_project_dir=override_project_dir,
previous_simulation_run=previous_simulation_run,
step_name=step_name,
in_imd_path=in_imd_path,
submission_system=submission_system,
initialize_first_run=initialize_first_run,
simulation_runs=simulation_runs,
equilibration_runs=equilibration_runs,
analysis_script=analysis_script,
_template_imd_path=_template_imd_path,
_no_double_submit_check=_no_double_submit_check,
verbose=verbose,
)
def run_liq(self):
# minsys_emin_liq, jobID
self.groSys_liq.imd = self.imd_liq_min
self.groSys_liq.prepare_for_simulation()
sys_emin_liq = simulation(
in_gromos_simulation_system=self.groSys_liq,
override_project_dir=self.groSys_liq.work_folder,
step_name="1_emin",
submission_system=self.submissonSystem_liq,
analysis_script=simulation_analysis.do,
verbose=self.verbose,
)
# eq
sys_emin_liq.imd = self.imd_liq_eq
sys_emin_liq.prepare_for_simulation()
sys_eq_liq = simulation(
in_gromos_simulation_system=sys_emin_liq,
override_project_dir=self.groSys_liq.work_folder,
step_name="2_eq",
submission_system=self.submissonSystem_liq,
analysis_script=simulation_analysis.do,
verbose=self.verbose,
)
# md
sys_eq_liq.imd = self.imd_liq_md
sys_eq_liq.prepare_for_simulation()
sys_md_liq = simulation(
in_gromos_simulation_system=sys_eq_liq,
override_project_dir=self.groSys_liq.work_folder,
step_name="3_sd",
submission_system=self.submissonSystem_liq,
analysis_script=simulation_analysis.do,
verbose=self.verbose,
)
self.groSys_liq_final = sys_md_liq
def run_gas(self):
# min
self.groSys_gas.imd = self.imd_gas_min
self.groSys_gas.prepare_for_simulation()
sys_emin_gas = simulation(
in_gromos_simulation_system=self.groSys_gas,
override_project_dir=self.groSys_gas.work_folder,
step_name="1_emin",
submission_system=self.submissonSystem_gas,
analysis_script=simulation_analysis.do,
verbose=self.verbose,
)
# eq
sys_emin_gas.imd = self.imd_gas_eq
sys_emin_gas.prepare_for_simulation()
sys_eq_gas = simulation(
in_gromos_simulation_system=sys_emin_gas,
override_project_dir=self.groSys_gas.work_folder,
step_name="2_eq",
submission_system=self.submissonSystem_gas,
analysis_script=simulation_analysis.do,
verbose=self.verbose,
)
# sd
sys_eq_gas.imd = self.imd_gas_eq
sys_eq_gas.prepare_for_simulation()
sys_sd_gas = simulation(
in_gromos_simulation_system=sys_eq_gas,
override_project_dir=self.groSys_gas.work_folder,
step_name="3_sd",
submission_system=self.submissonSystem_gas,
analysis_script=simulation_analysis.do,
verbose=self.verbose,
)
self.groSys_gas_final = sys_sd_gas
def _TI_lam_step(
in_gromos_system: Gromos_System,
project_dir: str,
step_name: str = "lam",
in_imd_path=None,
submission_system: _SubmissionSystem = LOCAL(),
simulation_runs: int = 1,
equilibration_runs: int = 0,
previous_simulation_run: int = None,
analysis_script: callable = simulation_analysis.do,
verbose: bool = True,
) -> Gromos_System:
template_control_dict = OrderedDict({
"concat": {
"do": True,
"sub": {
"cp_cnf": True,
"repair_NaN": True,
"cp_omd": True,
"cat_trc": True,
"cat_tre": True,
"cat_trg": True,
"convert_trcs": False,
},
},
"simulation_folder": {
"do": False,
"sub": {
"tar": False,
"remove": False
}
},
})
return simulation(
in_gromos_simulation_system=in_gromos_system,
override_project_dir=project_dir,
previous_simulation_run=previous_simulation_run,
step_name=step_name,
in_imd_path=in_imd_path,
submission_system=submission_system,
simulation_runs=simulation_runs,
equilibration_runs=equilibration_runs,
analysis_control_dict=template_control_dict,
analysis_script=analysis_script,
verbose=verbose,
)
def emin(
in_gromos_system: Gromos_System,
step_name: str = "emin",
override_project_dir: str = None,
in_imd_path=None,
submission_system: _SubmissionSystem = LOCAL(),
simulation_runs: int = 1,
equilibration_runs: int = 0,
previous_simulation_run: int = None,
_template_imd_path: str = template_emin,
_no_double_submit_check: bool = False,
initialize_first_run=False,
analysis_script: callable = simulation_analysis.do,
verbose: bool = True,
) -> Tuple[Gromos_System, int]:
template_emin_control_dict = simulation_analysis.template_control_dict
template_emin_control_dict["concat"]["cat_trc"] = False
template_emin_control_dict["concat"]["cat_tre"] = False
template_emin_control_dict["concat"]["cat_trg"] = False
if hasattr(in_gromos_system.imd, "WRITETRAJ"):
if in_gromos_system.imd.WRITETRAJ.NTWX > 0:
template_emin_control_dict["concat"]["cat_trc"] = False
if in_gromos_system.imd.WRITETRAJ.NTWE > 0:
template_emin_control_dict["concat"]["cat_tre"] = False
if in_gromos_system.imd.WRITETRAJ.NTWG > 0:
template_emin_control_dict["concat"]["cat_trg"] = False
return simulation(
in_gromos_simulation_system=in_gromos_system,
override_project_dir=override_project_dir,
previous_simulation_run=previous_simulation_run,
step_name=step_name,
in_imd_path=in_imd_path,
submission_system=submission_system,
initialize_first_run=initialize_first_run,
simulation_runs=simulation_runs,
equilibration_runs=equilibration_runs,
analysis_control_dict=template_emin_control_dict,
analysis_script=analysis_script,
_template_imd_path=_template_imd_path,
_no_double_submit_check=_no_double_submit_check,
verbose=verbose,
)
def equilibration_gromos_system_step(
self,
in_gromos_simulation_system: Gromos_System,
NTIVAL: int = 0,
NTISHI: int = 0,
TEMPI: float = 0,
TEMPO: float = 0,
prevID: int = -1,
run_name: str = "",
natoms: int = 0,
):
"""
Perform one step in equilibration routine
Parameters
----------
in_gromos_simulation_system : Gromos_System
Gromos System to work on
NTIVAL : int
NTIVAL Parameter to set
NTISHI : int
NTISHI Parameter to set
TEMPI : float
TEMPI Parameter to set
TEMPO : float
TEMPO Parameter to set
prevID : int
ID of previous run (for LSF Submission Syste)
run_name : str
Name of the current run (note needs to be unique for LSF not to crash)
natoms : int
Number of Atoms in the molecule
Returns
-------
md_sys : Gromos_System
Equilibrated gromos system
JobID : int
ID of the submitted job for the next job to wait on
"""
# adapt imd
eq_imd = Imd(template_md)
eq_imd.SYSTEM.NSM = 0
eq_imd.STEP.NSTLIM = 25000
multibath = MULTIBATH(
ALGORITHM=0, NBATHS=1, TEMP0=[TEMPO], TAU=[0.1], DOFSET=1, LAST=[natoms], COMBATH=[1], IRBATH=[1]
)
eq_imd.MULTIBATH = multibath
eq_imd.PRESSURESCALE.COUPLE = 1
eq_imd.FORCE.NEGR = 1
eq_imd.FORCE.NRE = [natoms]
eq_imd.NONBONDED.EPSRF = 4
eq_imd.NONBONDED.NSHAPE = -1
eq_imd.NONBONDED.NQEVAL = 100000
# add COVALENTFORM Block
covalentform = COVALENTFORM(NTBBH=0, NTBAH=0, NTBDN=0)
eq_imd.add_block(block=covalentform)
if self.amberscaling:
# Add AMBER Block
amber_block = AMBER(True, 1.2)
eq_imd.add_block(block=amber_block)
eq_imd.INITIALISE.IG = 3
eq_imd.INITIALISE.NTIVEL = NTIVAL
eq_imd.INITIALISE.NTISHI = NTISHI
eq_imd.INITIALISE.TEMPI = TEMPI
eq_imd.WRITETRAJ.NTWX = 500
eq_imd.WRITETRAJ.NTWE = 500
eq_imd.PRINTOUT.NTPR = 500
eq_imd.randomize_seed()
if prevID == -1:
md_sys = simulation(
in_gromos_simulation_system=in_gromos_simulation_system,
override_project_dir=self.groSys_liq.work_folder,
step_name="eq" + run_name,
in_imd_path=eq_imd,
submission_system=self._subsystem,
analysis_script=simulation_analysis.do,
verbose=self.verbose,
)
else:
md_sys = simulation(
in_gromos_simulation_system=in_gromos_simulation_system,
override_project_dir=self.groSys_liq.work_folder,
step_name="eq" + run_name,
in_imd_path=eq_imd,
submission_system=self._subsystem,
analysis_script=simulation_analysis.do,
verbose=self.verbose,
previous_simulation_run=prevID,
)
return md_sys, md_sys._last_jobID