1 #!/bin/env python
2 #
3 # File: OpenMMPerformMDSimulation.py
4 # Author: Manish Sud <msud@san.rr.com>
5 #
6 # Copyright (C) 2025 Manish Sud. All rights reserved.
7 #
8 # The functionality available in this script is implemented using OpenMM, an
9 # open source molecuar simulation package.
10 #
11 # This file is part of MayaChemTools.
12 #
13 # MayaChemTools is free software; you can redistribute it and/or modify it under
14 # the terms of the GNU Lesser General Public License as published by the Free
15 # Software Foundation; either version 3 of the License, or (at your option) any
16 # later version.
17 #
18 # MayaChemTools is distributed in the hope that it will be useful, but without
19 # any warranty; without even the implied warranty of merchantability of fitness
20 # for a particular purpose. See the GNU Lesser General Public License for more
21 # details.
22 #
23 # You should have received a copy of the GNU Lesser General Public License
24 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
25 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
26 # Boston, MA, 02111-1307, USA.
27 #
28
29 from __future__ import print_function
30
31 # Add local python path to the global path and import standard library modules...
32 import os
33 import sys; sys.path.insert(0, os.path.join(os.path.dirname(sys.argv[0]), "..", "lib", "Python"))
34 import time
35 import re
36
37 # OpenMM imports...
38 try:
39 import openmm as mm
40 import openmm.app
41 except ImportError as ErrMsg:
42 sys.stderr.write("\nFailed to import OpenMM related module/package: %s\n" % ErrMsg)
43 sys.stderr.write("Check/update your OpenMM environment and try again.\n\n")
44 sys.exit(1)
45
46 # MDTraj import...
47 try:
48 import mdtraj
49 except ImportError as ErrMsg:
50 sys.stderr.write("\nFailed to import MDTraj: %s\n" % ErrMsg)
51 sys.stderr.write("Check/update your MDTraj environment and try again.\n\n")
52 sys.exit(1)
53
54 # MayaChemTools imports...
55 try:
56 from docopt import docopt
57 import MiscUtil
58 import OpenMMUtil
59 except ImportError as ErrMsg:
60 sys.stderr.write("\nFailed to import MayaChemTools module/package: %s\n" % ErrMsg)
61 sys.stderr.write("Check/update your MayaChemTools environment and try again.\n\n")
62 sys.exit(1)
63
64 ScriptName = os.path.basename(sys.argv[0])
65 Options = {}
66 OptionsInfo = {}
67
68 def main():
69 """Start execution of the script."""
70
71 MiscUtil.PrintInfo("\n%s (OpenMM v%s; MayaChemTools v%s; %s): Starting...\n" % (ScriptName, mm.Platform.getOpenMMVersion(), MiscUtil.GetMayaChemToolsVersion(), time.asctime()))
72
73 (WallClockTime, ProcessorTime) = MiscUtil.GetWallClockAndProcessorTime()
74
75 # Retrieve command line arguments and options...
76 RetrieveOptions()
77
78 # Process and validate command line arguments and options...
79 ProcessOptions()
80
81 # Perform actions required by the script...
82 PerformMDSimulation()
83
84 MiscUtil.PrintInfo("\n%s: Done...\n" % ScriptName)
85 MiscUtil.PrintInfo("Total time: %s" % MiscUtil.GetFormattedElapsedTime(WallClockTime, ProcessorTime))
86
87 def PerformMDSimulation():
88 """Perform MD simulation."""
89
90 # Prepare system for simulation...
91 System, Topology, Positions = PrepareSystem()
92
93 # Freeze and restraint atoms...
94 FreezeRestraintAtoms(System, Topology, Positions)
95
96 # Setup integrator...
97 Integrator = SetupIntegrator()
98
99 # Setup simulation...
100 Simulation = SetupSimulation(System, Integrator, Topology, Positions)
101
102 # Write setup files...
103 WriteSimulationSetupFiles(System, Integrator)
104
105 # Perform minimization...
106 PerformMinimization(Simulation)
107
108 # Set up intial velocities...
109 SetupInitialVelocities(Simulation)
110
111 # Perform equilibration...
112 PerformEquilibration(Simulation)
113
114 # Setup reporters for production run...
115 SetupReporters(Simulation)
116
117 # Perform or restart production run...
118 PerformOrRestartProductionRun(Simulation)
119
120 # Save final state files...
121 WriteFinalStateFiles(Simulation)
122
123 # Reimage and realign trajectory for periodic systems...
124 ProcessTrajectory(System, Topology)
125
126 def PrepareSystem():
127 """Prepare system for simulation."""
128
129 System, Topology, Positions = OpenMMUtil.InitializeSystem(OptionsInfo["Infile"], OptionsInfo["ForcefieldParams"], OptionsInfo["SystemParams"], OptionsInfo["WaterBox"], OptionsInfo["WaterBoxParams"], OptionsInfo["SmallMolFile"], OptionsInfo["SmallMolID"])
130
131 if OptionsInfo["NPTMode"]:
132 BarostatHandle = OpenMMUtil.InitializeBarostat(OptionsInfo["IntegratorParams"])
133 MiscUtil.PrintInfo("Adding barostat to system for NPT simulation...")
134 try:
135 System.addForce(BarostatHandle)
136 except Exception as ErrMsg:
137 MiscUtil.PrintInfo("")
138 MiscUtil.PrintError("Failed to add barostat:\n%s\n" % (ErrMsg))
139
140 # Write out a PDB file for the system...
141 PDBFile = OptionsInfo["PDBOutfile"]
142 if OptionsInfo["RestartMode"]:
143 MiscUtil.PrintInfo("\nSkipping wrriting of PDB file %s during restart..." % PDBFile)
144 else:
145 MiscUtil.PrintInfo("\nWriting PDB file %s..." % PDBFile)
146 OpenMMUtil.WritePDBFile(PDBFile, Topology, Positions, OptionsInfo["OutputParams"]["PDBOutKeepIDs"])
147
148 return (System, Topology, Positions)
149
150 def SetupIntegrator():
151 """Setup integrator. """
152
153 Integrator = OpenMMUtil.InitializeIntegrator(OptionsInfo["IntegratorParams"], OptionsInfo["SystemParams"]["ConstraintErrorTolerance"])
154
155 return Integrator
156
157 def SetupSimulation(System, Integrator, Topology, Positions):
158 """Setup simulation. """
159
160 Simulation = OpenMMUtil.InitializeSimulation(System, Integrator, Topology, Positions, OptionsInfo["PlatformParams"])
161
162 return Simulation
163
164 def SetupInitialVelocities(Simulation):
165 """Setup initial velocities."""
166
167 # Set velocities to random values choosen from a Boltzman distribution at a given
168 # temperature...
169 if OptionsInfo["RestartMode"]:
170 MiscUtil.PrintInfo("\nSkipping settting of intial velocities to temperature during restart...")
171 else:
172 MiscUtil.PrintInfo("\nSettting intial velocities to temperature...")
173 IntegratorParamsInfo = OpenMMUtil.SetupIntegratorParameters(OptionsInfo["IntegratorParams"])
174 Simulation.context.setVelocitiesToTemperature(IntegratorParamsInfo["Temperature"])
175
176 def PerformMinimization(Simulation):
177 """Perform minimization."""
178
179 SimulationParams = OpenMMUtil.SetupSimulationParameters(OptionsInfo["SimulationParams"])
180
181 if OptionsInfo["RestartMode"]:
182 MiscUtil.PrintInfo("\nSkipping energy minimization during restart...")
183 return
184 else:
185 if not SimulationParams["Minimization"]:
186 MiscUtil.PrintInfo("\nSkipping energy minimization...")
187 return
188
189 OutputParams = OptionsInfo["OutputParams"]
190
191 # Setup a local minimization reporter...
192 MinimizeReporter = None
193 if OutputParams["MinimizationDataStdout"] or OutputParams["MinimizationDataLog"]:
194 MinimizeReporter = LocalMinimizationReporter()
195
196 if MinimizeReporter is not None:
197 MiscUtil.PrintInfo("\nAdding minimization reporters...")
198 if OutputParams["MinimizationDataLog"]:
199 MiscUtil.PrintInfo("Adding data log minimization reporter (Steps: %s; File: %s)..." % (OutputParams["MinimizationDataSteps"], OutputParams["MinimizationDataLogFile"]))
200 if OutputParams["MinimizationDataStdout"]:
201 MiscUtil.PrintInfo("Adding data stdout minimization reporter (Steps: %s)..." % (OutputParams["MinimizationDataSteps"]))
202 else:
203 MiscUtil.PrintInfo("\nSkipping addition of minimization reporters...")
204
205 MaxSteps = SimulationParams["MinimizationMaxSteps"]
206
207 MaxStepsMsg = "MaxSteps: %s" % ("UntilConverged" if MaxSteps == 0 else MaxSteps)
208 ToleranceMsg = "Tolerance: %.2f kcal/mol/A (%.2f kjoules/mol/nm)" % (SimulationParams["MinimizationToleranceInKcal"], SimulationParams["MinimizationToleranceInJoules"])
209
210 MiscUtil.PrintInfo("\nPerforming energy minimization (%s; %s)..." % (MaxStepsMsg, ToleranceMsg))
211
212 if OutputParams["MinimizationDataStdout"]:
213 HeaderLine = SetupMinimizationDataOutHeaderLine()
214 print("\n%s" % HeaderLine)
215
216 Simulation.minimizeEnergy(tolerance = SimulationParams["MinimizationTolerance"], maxIterations = MaxSteps, reporter = MinimizeReporter)
217
218 if OutputParams["MinimizationDataLog"]:
219 WriteMinimizationDataLogFile(MinimizeReporter.DataOutValues)
220
221 if OutputParams["PDBOutMinimized"]:
222 MiscUtil.PrintInfo("\nWriting PDB file %s..." % OptionsInfo["MinimizedPDBOutfile"])
223 OpenMMUtil.WriteSimulationStatePDBFile(Simulation, OptionsInfo["MinimizedPDBOutfile"], OutputParams["PDBOutKeepIDs"])
224
225 def PerformEquilibration(Simulation):
226 """Perform equilibration."""
227
228 Mode = OptionsInfo["Mode"]
229 SimulationParams = OptionsInfo["SimulationParams"]
230 OutputParams = OptionsInfo["OutputParams"]
231
232 if OptionsInfo["RestartMode"]:
233 MiscUtil.PrintInfo("\nSkipping equilibration during restart...")
234 return
235 else:
236 if not SimulationParams["Equilibration"]:
237 MiscUtil.PrintInfo("\nSkipping equilibration...")
238 return
239
240 EquilibrationSteps = SimulationParams["EquilibrationSteps"]
241
242 IntegratorParamsInfo = OpenMMUtil.SetupIntegratorParameters(OptionsInfo["IntegratorParams"])
243 StepSize = IntegratorParamsInfo["StepSize"]
244
245 TotalTime = OpenMMUtil.GetFormattedTotalSimulationTime(StepSize, EquilibrationSteps)
246 MiscUtil.PrintInfo("\nPerforming equilibration (Mode: %s; Steps: %s; StepSize: %s; TotalTime: %s)..." % (Mode, EquilibrationSteps, StepSize, TotalTime))
247
248 # Equilibrate...
249 Simulation.step(EquilibrationSteps)
250
251 if OutputParams["PDBOutEquilibrated"]:
252 MiscUtil.PrintInfo("\nWriting PDB file %s..." % OptionsInfo["EquilibratedPDBOutfile"])
253 OpenMMUtil.WriteSimulationStatePDBFile(Simulation, OptionsInfo["EquilibratedPDBOutfile"], OutputParams["PDBOutKeepIDs"])
254
255 def PerformOrRestartProductionRun(Simulation):
256 """Perform or restart production run. """
257
258 if OptionsInfo["RestartMode"]:
259 RestartProductionRun(Simulation)
260 else:
261 PerformProductionRun(Simulation)
262
263 def PerformProductionRun(Simulation):
264 """Perform production run."""
265
266 Mode = OptionsInfo["Mode"]
267 SimulationParams = OptionsInfo["SimulationParams"]
268 Steps = SimulationParams["Steps"]
269
270 IntegratorParamsInfo = OpenMMUtil.SetupIntegratorParameters(OptionsInfo["IntegratorParams"])
271 StepSize = IntegratorParamsInfo["StepSize"]
272
273 if SimulationParams["Equilibration"]:
274 Simulation.currentStep = 0
275 Simulation.context.setTime(0.0 * mm.unit.picoseconds)
276 MiscUtil.PrintInfo("\nSetting current step and current time to 0 for starting production run after equilibration...")
277
278 TotalTime = OpenMMUtil.GetFormattedTotalSimulationTime(StepSize, Steps)
279 MiscUtil.PrintInfo("\nPerforming production run (Mode: %s; Steps: %s; StepSize: %s; TotalTime: %s)..." % (Mode, Steps, StepSize, TotalTime))
280
281 Simulation.step(Steps)
282
283 def RestartProductionRun(Simulation):
284 """Restart production run."""
285
286 SimulationParams = OptionsInfo["SimulationParams"]
287 RestartParams = OptionsInfo["RestartParams"]
288
289 RestartFile = RestartParams["FinalStateFile"]
290
291 Steps = SimulationParams["Steps"]
292
293 IntegratorParamsInfo = OpenMMUtil.SetupIntegratorParameters(OptionsInfo["IntegratorParams"])
294 StepSize = IntegratorParamsInfo["StepSize"]
295
296 TotalTime = OpenMMUtil.GetFormattedTotalSimulationTime(StepSize, Steps)
297 MiscUtil.PrintInfo("\nRestarting production run (Steps: %s; StepSize: %s; TotalTime: %s)..." % (Steps, StepSize, TotalTime))
298
299 if RestartParams["FinalStateFileCheckpointMode"]:
300 MiscUtil.PrintInfo("Loading final state checkpoint file %s...\n" % RestartFile)
301 Simulation.loadCheckpoint(RestartFile)
302 elif RestartParams["FinalStateFileXMLMode"]:
303 MiscUtil.PrintInfo("Loading final state XML f ile %s...\n" % RestartFile)
304 Simulation.loadState(RestartFile)
305 else:
306 MiscUtil.PrintError("The specified final state restart file, %s, is not a valid. Supported file formats: chk or xml" % (RestartFile))
307
308 Simulation.step(Steps)
309
310 def SetupReporters(Simulation):
311 """Setup reporters. """
312
313 (TrajReporter, DataLogReporter, DataStdoutReporter, CheckpointReporter) = OpenMMUtil.InitializeReporters(OptionsInfo["OutputParams"], OptionsInfo["SimulationParams"]["Steps"], OptionsInfo["DataOutAppendMode"])
314
315 if TrajReporter is None and DataLogReporter is None and DataStdoutReporter is None and CheckpointReporter is None:
316 MiscUtil.PrintInfo("\nSkip adding reporters...")
317 return
318
319 MiscUtil.PrintInfo("\nAdding reporters...")
320
321 OutputParams = OptionsInfo["OutputParams"]
322 AppendMsg = ""
323 if OptionsInfo["RestartMode"]:
324 AppendMsg = "; Append: Yes" if OptionsInfo["DataOutAppendMode"] else "; Append: No"
325 if TrajReporter is not None:
326 MiscUtil.PrintInfo("Adding trajectory reporter (Steps: %s; File: %s%s)..." % (OutputParams["TrajSteps"], OutputParams["TrajFile"], AppendMsg))
327 Simulation.reporters.append(TrajReporter)
328
329 if CheckpointReporter is not None:
330 MiscUtil.PrintInfo("Adding checkpoint reporter (Steps: %s; File: %s)..." % (OutputParams["CheckpointSteps"], OutputParams["CheckpointFile"]))
331 Simulation.reporters.append(CheckpointReporter)
332
333 if DataLogReporter is not None:
334 MiscUtil.PrintInfo("Adding data log reporter (Steps: %s; File: %s%s)..." % (OutputParams["DataLogSteps"], OutputParams["DataLogFile"], AppendMsg))
335 Simulation.reporters.append(DataLogReporter)
336
337 if DataStdoutReporter is not None:
338 MiscUtil.PrintInfo("Adding data stdout reporter (Steps: %s)..." % (OutputParams["DataStdoutSteps"]))
339 Simulation.reporters.append(DataStdoutReporter)
340
341 class LocalMinimizationReporter(mm.MinimizationReporter):
342 """Setup a local minimization reporter. """
343
344 (DataSteps, DataOutTypeList, DataOutDelimiter, StdoutStatus) = [None] * 4
345
346 DataOutValues = []
347 First = True
348
349 def report(self, Iteration, PositonsList, GradientsList, DataStatisticsMap):
350 """Report and track minimization."""
351
352 if self.First:
353 # Initialize...
354 self.DataSteps = OptionsInfo["OutputParams"]["MinimizationDataSteps"]
355 self.DataOutTypeList = OptionsInfo["OutputParams"]["MinimizationDataOutTypeOpenMMNameList"]
356 self.DataOutDelimiter = OptionsInfo["OutputParams"]["DataOutDelimiter"]
357 self.StdoutStatus = True if OptionsInfo["OutputParams"]["MinimizationDataStdout"] else False
358
359 self.First = False
360
361 if Iteration % self.DataSteps == 0:
362 # Setup data values...
363 DataValues = []
364 DataValues.append("%s" % Iteration)
365 for DataType in self.DataOutTypeList:
366 DataValue = "%.4f" % DataStatisticsMap[DataType]
367 DataValues.append(DataValue)
368
369 # Track data...
370 self.DataOutValues.append(DataValues)
371
372 # Print data values...
373 if self.StdoutStatus:
374 print("%s" % self.DataOutDelimiter.join(DataValues))
375
376 # This method must return a bool. You may return true for early termination.
377 return False
378
379 def WriteMinimizationDataLogFile(DataOutValues):
380 """Write minimization data log file. """
381
382 OutputParams = OptionsInfo["OutputParams"]
383
384 Outfile = OutputParams["MinimizationDataLogFile"]
385 OutDelimiter = OutputParams["DataOutDelimiter"]
386
387 MiscUtil.PrintInfo("\nWriting minimization log file %s..." % Outfile)
388 OutFH = open(Outfile, "w")
389
390 HeaderLine = SetupMinimizationDataOutHeaderLine()
391 OutFH.write("%s\n" % HeaderLine)
392
393 for LineWords in DataOutValues:
394 Line = OutDelimiter.join(LineWords)
395 OutFH.write("%s\n" % Line)
396
397 OutFH.close()
398
399 def SetupMinimizationDataOutHeaderLine():
400 """Setup minimization data output header line. """
401
402 LineWords = ["Iteration"]
403 for Label in OptionsInfo["OutputParams"]["MinimizationDataOutTypeList"]:
404 if re.match("^(SystemEnergy|RestraintEnergy)$", Label, re.I):
405 LineWords.append("%s(kjoules/mol)" % Label)
406 elif re.match("^RestraintStrength$", Label, re.I):
407 LineWords.append("%s(kjoules/mol/nm^2)" % Label)
408 else:
409 LineWords.append(Label)
410
411 Line = OptionsInfo["OutputParams"]["DataOutDelimiter"].join(LineWords)
412
413 return Line
414
415 def FreezeRestraintAtoms(System, Topology, Positions):
416 """Handle freezing and restraining of atoms."""
417
418 # Get atoms for freezing...
419 FreezeAtomList = None
420 if OptionsInfo["FreezeAtoms"]:
421 FreezeAtomList = OpenMMUtil.GetAtoms(Topology, OptionsInfo["FreezeAtomsParams"]["CAlphaProteinStatus"], OptionsInfo["FreezeAtomsParams"]["ResidueNames"], OptionsInfo["FreezeAtomsParams"]["Negate"])
422 if FreezeAtomList is None:
423 MiscUtil.PrintError("The freeze atoms parameters specified, \"selection, %s, selectionSpec, %s, negate, %s\", - using \"--freezeAtomsParams\" option didn't match any atoms in the system. You must specify a valid set of parameters for freezing atoms or disable freezing using \"No\" value for \"--freezeAtoms\" option.." % (OptionsInfo["FreezeAtomsParams"]["Selection"], OptionsInfo["FreezeAtomsParams"]["SelectionSpec"], OptionsInfo["FreezeAtomsParams"]["Negate"]))
424
425 # Get atoms for restraining...
426 RestraintAtomList = None
427 if OptionsInfo["RestraintAtoms"]:
428 RestraintAtomList = OpenMMUtil.GetAtoms(Topology, OptionsInfo["RestraintAtomsParams"]["CAlphaProteinStatus"], OptionsInfo["RestraintAtomsParams"]["ResidueNames"], OptionsInfo["RestraintAtomsParams"]["Negate"])
429 if RestraintAtomList is None:
430 MiscUtil.PrintError("The restraint atoms parameters specified, \"selection, %s, selectionSpec, %s, negate, %s\", - using \"--restraintAtomsParams\" option didn't match any atoms in the system. You must specify a valid set of parameters for restraining atoms or disable restraining using \"No\" value for \"--restraintAtoms\" option." % (OptionsInfo["RestraintAtomsParams"]["Selection"], OptionsInfo["RestraintAtomsParams"]["SelectionSpec"], OptionsInfo["RestraintAtomsParams"]["Negate"]))
431
432 # Check for atoms to freeze or restraint...
433 if FreezeAtomList is None and RestraintAtomList is None:
434 return
435
436 # Check for overlap between freeze and restraint atoms...
437 if OpenMMUtil.DoAtomListsOverlap(FreezeAtomList, RestraintAtomList):
438 MiscUtil.PrintError("The atoms specified using \"--freezeAtomsParams\" and \"--restraintAtomsParams\" options appear to overlap. You must specify unique sets of atoms to freeze and restraint.")
439
440 # Check overlap of freeze atoms with system constraints...
441 if OpenMMUtil.DoesAtomListOverlapWithSystemConstraints(System, FreezeAtomList):
442 MiscUtil.PrintError("The atoms specified using \"--freezeAtomsParams\" appear to overlap with atoms being constrained corresponding to the value specified, %s, for paramater name \"constraints\" using \"--systemParams\" option.\n\nYou must specify a unique set of atoms to freeze or turn off system constaints by specifying value, None, for \"constraints\" parameter using option \"--systemsParams\".\n\nIn addtion, you may want specify, no, value for \"rigidWater\" option.\n\nThe atoms are frozen by setting their particle mass to zero. OpenMM doesn't allow to both constraint atoms and set their mass to zero." % (OptionsInfo["SystemParams"]["Constraints"]))
443
444 # Check overlap of restraint atoms with system constraints...
445 if OpenMMUtil.DoesAtomListOverlapWithSystemConstraints(System, RestraintAtomList):
446 MiscUtil.PrintInfo("")
447 MiscUtil.PrintWarning("The atoms specified using \"--restraintAtomsParams\" appear to overlap with atoms being constrained corresponding to the value specified, %s, for paramater name \"constraints\" using \"--systemParams\" option. You may want to specify a unique set of atoms to restraints or turn off system constaints by specifying value, None, for \"constraints\" parameter using option \"--systemsParams\"." % (OptionsInfo["SystemParams"]["Constraints"]))
448
449 # Check and adjust step size...
450 if FreezeAtomList is not None or RestraintAtomList is not None:
451 CheckAndAdjustStepSizeDuringFreezeRestraintAtoms()
452
453 # Freeze atoms...
454 if FreezeAtomList is None:
455 MiscUtil.PrintInfo("\nSkipping freezing of atoms...")
456 else:
457 MiscUtil.PrintInfo("\nFreezing atoms (Selection: %s)..." % OptionsInfo["FreezeAtomsParams"]["Selection"])
458 OpenMMUtil.FreezeAtoms(System, FreezeAtomList)
459
460 # Restraint atoms...
461 if RestraintAtomList is None:
462 MiscUtil.PrintInfo("\nSkipping restraining of atoms...")
463 else:
464 MiscUtil.PrintInfo("\nRestraining atoms (Selection: %s)..." % OptionsInfo["RestraintAtomsParams"]["Selection"])
465
466 SprintConstantInKcal = OptionsInfo["RestraintSpringConstant"]
467 OpenMMUtil.RestraintAtoms(System, Positions, RestraintAtomList, SprintConstantInKcal)
468
469 def CheckAndAdjustStepSizeDuringFreezeRestraintAtoms():
470 """Check and set step size during freezing or restraining of atoms """
471
472 if re.match("^auto$", OptionsInfo["IntegratorParams"]["StepSizeSpecified"], re.I):
473 # Automatically set stepSize to 2.0 fs..
474 OptionsInfo["IntegratorParams"]["StepSize"] = 2.0
475 MiscUtil.PrintInfo("")
476 MiscUtil.PrintWarning("The time step has been automatically set to %s fs during freezing or restraining of atoms. You may specify an explicit value for parameter name, stepSize, using \"--integratorParams\" option." % (OptionsInfo["IntegratorParams"]["StepSize"]))
477 elif OptionsInfo["IntegratorParams"]["StepSize"] > 2:
478 MiscUtil.PrintInfo("")
479 MiscUtil.PrintWarning("A word to the wise: The parameter value specified, %s, for parameter name, stepSize, using \"--integratorParams\" option may be too large. You may want to consider using a smaller time step. Othwerwise, your simulation may blow up." % (OptionsInfo["IntegratorParams"]["StepSize"] ))
480 MiscUtil.PrintInfo("")
481
482 def WriteSimulationSetupFiles(System, Integrator):
483 """Write simulation setup files for system and integrator."""
484
485 OutputParams = OptionsInfo["OutputParams"]
486
487 if OutputParams["XmlSystemOut"] or OutputParams["XmlIntegratorOut"]:
488 MiscUtil.PrintInfo("")
489
490 if OutputParams["XmlSystemOut"]:
491 Outfile = OutputParams["XmlSystemFile"]
492 MiscUtil.PrintInfo("Writing system setup XML file %s..." % Outfile)
493 with open(Outfile, mode = "w") as OutFH:
494 OutFH.write(mm.XmlSerializer.serialize(System))
495
496 if OutputParams["XmlIntegratorOut"]:
497 Outfile = OutputParams["XmlIntegratorFile"]
498 MiscUtil.PrintInfo("Writing integrator setup XML file %s..." % Outfile)
499 with open(Outfile, mode = "w") as OutFH:
500 OutFH.write(mm.XmlSerializer.serialize(Integrator))
501
502 def WriteFinalStateFiles(Simulation):
503 """Write final state files. """
504
505 OutputParams = OptionsInfo["OutputParams"]
506
507 if OutputParams["SaveFinalStateCheckpoint"] or OutputParams["SaveFinalStateXML"] or OutputParams["PDBOutFinal"]:
508 MiscUtil.PrintInfo("")
509
510 if OutputParams["SaveFinalStateCheckpoint"]:
511 Outfile = OutputParams["SaveFinalStateCheckpointFile"]
512 MiscUtil.PrintInfo("Writing final state checkpoint file %s..." % Outfile)
513 Simulation.saveCheckpoint(Outfile)
514
515 if OutputParams["SaveFinalStateXML"]:
516 Outfile = OutputParams["SaveFinalStateXMLFile"]
517 MiscUtil.PrintInfo("Writing final state XML file %s..." % Outfile)
518 Simulation.saveState(Outfile)
519
520 if OutputParams["PDBOutFinal"]:
521 MiscUtil.PrintInfo("\nWriting PDB file %s..." % OptionsInfo["FinalPDBOutfile"])
522 OpenMMUtil.WriteSimulationStatePDBFile(Simulation, OptionsInfo["FinalPDBOutfile"], OutputParams["PDBOutKeepIDs"])
523
524 def ProcessTrajectory(System, Topology):
525 """Reimage and realign trajectory for periodic systems. """
526
527 ReimageFrames = True if OpenMMUtil.DoesSystemUsesPeriodicBoundaryConditions(System) else False
528 if not ReimageFrames:
529 MiscUtil.PrintInfo("\nSkipping reimaging and realigning of trajectory for a system not using periodic boundary conditions...")
530 return
531
532 MiscUtil.PrintInfo("\nReimaging and realigning trajectory for a system using periodic boundary conditions...")
533
534 # Reimage and realign trajectory file...
535 RealignFrames = True
536 TrajTopologyFile = OptionsInfo["PDBOutfile"]
537 TrajFile = OptionsInfo["OutputParams"]["TrajFile"]
538 Traj, ReimagedStatus, RealignedStatus = OpenMMUtil.ReimageRealignTrajectory(Topology, TrajFile, ReimageFrames, RealignFrames)
539
540 if (Traj is None) or (not ReimagedStatus and not RealignedStatus):
541 MiscUtil.PrintInfo("Skipping writing first frame to PDB file %s..." % PDBOutfile)
542 MiscUtil.PrintInfo("Skippig writing trajectory file %s..." % TrajOutfile)
543 return
544
545 PDBOutFormat = OptionsInfo["OutputParams"]["PDBOutFormat"]
546 PDBOutfile = OptionsInfo["ReimagedPDBOutfile"]
547 TrajOutfile = OptionsInfo["ReimagedTrajOutfile"]
548
549 # Write out first frame...
550 MiscUtil.PrintInfo("Writing first frame to PDB file %s..." % PDBOutfile)
551 if re.match("^CIF$", PDBOutFormat, re.I):
552 # MDTraj doesn't appear to support CIF format. Write it out as a temporary
553 # PDB file and convert it using OpenMM...
554 FileDir, FileRoot, FileExt = MiscUtil.ParseFileName(PDBOutfile)
555 TmpPDBOutfile = "%s_PID%s.pdb" % (FileRoot, os.getpid())
556 Traj[0].save(TmpPDBOutfile)
557
558 PDBHandle = OpenMMUtil.ReadPDBFile(TmpPDBOutfile)
559 OpenMMUtil.WritePDBFile(PDBOutfile, PDBHandle.topology, PDBHandle.positions, OptionsInfo["OutputParams"]["PDBOutKeepIDs"])
560
561 os.remove(TmpPDBOutfile)
562 else:
563 Traj[0].save(PDBOutfile)
564
565 # Write out reimaged and realinged trajectory...
566 MiscUtil.PrintInfo("Writing trajectory file %s..." % TrajOutfile)
567 Traj.save(TrajOutfile)
568
569 def ProcessOutfilePrefixParameter():
570 """Process outfile prefix paramater."""
571
572 OutfilePrefix = Options["--outfilePrefix"]
573
574 if not re.match("^auto$", OutfilePrefix, re.I):
575 OptionsInfo["OutfilePrefix"] = OutfilePrefix
576 return
577
578 if OptionsInfo["SmallMolFileMode"]:
579 OutfilePrefix = "%s_%s_Complex" % (OptionsInfo["InfileRoot"], OptionsInfo["SmallMolFileRoot"])
580 else:
581 OutfilePrefix = "%s" % (OptionsInfo["InfileRoot"])
582
583 if re.match("^yes$", Options["--waterBox"], re.I):
584 OutfilePrefix = "%s_Solvated" % (OutfilePrefix)
585
586 OutfilePrefix = "%s_%s" % (OutfilePrefix, OptionsInfo["Mode"])
587
588 OptionsInfo["OutfilePrefix"] = OutfilePrefix
589
590 def ProcessOutfileNames():
591 """Process outfile names."""
592
593 OutputParams = OptionsInfo["OutputParams"]
594 OutfileParamNames = ["CheckpointFile", "DataLogFile", "MinimizationDataLogFile", "SaveFinalStateCheckpointFile", "SaveFinalStateXMLFile", "TrajFile", "XmlSystemFile", "XmlIntegratorFile"]
595 for OutfileParamName in OutfileParamNames:
596 OutfileParamValue = OutputParams[OutfileParamName]
597 if not Options["--overwrite"]:
598 if os.path.exists(OutfileParamValue):
599 MiscUtil.PrintError("The file specified, %s, for parameter name, %s, using option \"--outfileParams\" already exist. Use option \"--ov\" or \"--overwrite\" and try again. " % (OutfileParamValue, OutfileParamName))
600
601 PDBOutfile = "%s.%s" % (OptionsInfo["OutfilePrefix"], OutputParams["PDBOutfileExt"])
602 ReimagedPDBOutfile = "%s_Reimaged.%s" % (OptionsInfo["OutfilePrefix"], OutputParams["PDBOutfileExt"])
603 ReimagedTrajOutfile = "%s_Reimaged.%s" % (OptionsInfo["OutfilePrefix"], OutputParams["TrajFileExt"])
604
605 MinimizedPDBOutfile = "%s_Minimized.%s" % (OptionsInfo["OutfilePrefix"], OutputParams["PDBOutfileExt"])
606 EquilibratedPDBOutfile = "%s_Equilibrated.%s" % (OptionsInfo["OutfilePrefix"], OutputParams["PDBOutfileExt"])
607 FinalPDBOutfile = "%s_Final.%s" % (OptionsInfo["OutfilePrefix"], OutputParams["PDBOutfileExt"])
608
609 for Outfile in [PDBOutfile, ReimagedPDBOutfile, ReimagedTrajOutfile, MinimizedPDBOutfile, EquilibratedPDBOutfile, FinalPDBOutfile]:
610 if not Options["--overwrite"]:
611 if os.path.exists(Outfile):
612 MiscUtil.PrintError("The file name, %s, generated using option \"--outfilePrefix\" already exist. Use option \"--ov\" or \"--overwrite\" and try again. " % (Outfile))
613 OptionsInfo["PDBOutfile"] = PDBOutfile
614 OptionsInfo["ReimagedPDBOutfile"] = ReimagedPDBOutfile
615 OptionsInfo["ReimagedTrajOutfile"] = ReimagedTrajOutfile
616
617 OptionsInfo["MinimizedPDBOutfile"] = MinimizedPDBOutfile
618 OptionsInfo["EquilibratedPDBOutfile"] = EquilibratedPDBOutfile
619 OptionsInfo["FinalPDBOutfile"] = FinalPDBOutfile
620
621 def ProcessRestartParameters():
622 """Process restart parameters. """
623
624 OptionsInfo["RestartMode"] = True if re.match("^yes$", Options["--restart"], re.I) else False
625 OptionsInfo["RestartParams"] = OpenMMUtil.ProcessOptionOpenMMRestartParameters("--restartParams", Options["--restartParams"], OptionsInfo["OutfilePrefix"])
626 if OptionsInfo["RestartMode"]:
627 RestartFile = OptionsInfo["RestartParams"]["FinalStateFile"]
628 if not os.path.exists(RestartFile):
629 MiscUtil.PrintError("The file specified, %s, for parameter name, finalStateFile, using option \"--restartParams\" doesn't exist." % (RestartFile))
630
631 DataOutAppendMode = False
632 if OptionsInfo["RestartMode"]:
633 DataOutAppendMode = True if OptionsInfo["RestartParams"]["DataAppend"] else False
634 OptionsInfo["DataOutAppendMode"] = DataOutAppendMode
635
636 def ProcessWaterBoxParameters():
637 """Process water box parameters. """
638
639 OptionsInfo["WaterBox"] = True if re.match("^yes$", Options["--waterBox"], re.I) else False
640 OptionsInfo["WaterBoxParams"] = OpenMMUtil.ProcessOptionOpenMMWaterBoxParameters("--waterBoxParams", Options["--waterBoxParams"])
641
642 if OptionsInfo["WaterBox"]:
643 if OptionsInfo["ForcefieldParams"]["ImplicitWater"]:
644 MiscUtil.PrintInfo("")
645 MiscUtil.PrintWarning("The value, %s, specified using option \"--waterBox\" may not be valid for the combination of biopolymer and water forcefields, %s and %s, specified using \"--forcefieldParams\". You may consider using a valid combination of biopolymer and water forcefields for explicit water during the addition of a water box." % (Options["--waterBox"], OptionsInfo["ForcefieldParams"]["Biopolymer"], OptionsInfo["ForcefieldParams"]["Water"]))
646
647 def ProcessOptions():
648 """Process and validate command line arguments and options."""
649
650 MiscUtil.PrintInfo("Processing options...")
651
652 ValidateOptions()
653
654 OptionsInfo["Infile"] = Options["--infile"]
655 FileDir, FileName, FileExt = MiscUtil.ParseFileName(OptionsInfo["Infile"])
656 OptionsInfo["InfileRoot"] = FileName
657
658 SmallMolFile = Options["--smallMolFile"]
659 SmallMolID = Options["--smallMolID"]
660 SmallMolFileMode = False
661 SmallMolFileRoot = None
662 if SmallMolFile is not None:
663 FileDir, FileName, FileExt = MiscUtil.ParseFileName(SmallMolFile)
664 SmallMolFileRoot = FileName
665 SmallMolFileMode = True
666
667 OptionsInfo["SmallMolFile"] = SmallMolFile
668 OptionsInfo["SmallMolFileRoot"] = SmallMolFileRoot
669 OptionsInfo["SmallMolFileMode"] = SmallMolFileMode
670 OptionsInfo["SmallMolID"] = SmallMolID.upper()
671
672 OptionsInfo["Mode"] = Options["--mode"].upper()
673 OptionsInfo["NPTMode"] = True if re.match("^NPT$", OptionsInfo["Mode"]) else False
674 OptionsInfo["NVTMode"] = True if re.match("^NVT$", OptionsInfo["Mode"]) else False
675
676 ProcessOutfilePrefixParameter()
677
678 if OptionsInfo["NVTMode"]:
679 ParamsDefaultInfoOverride = {"DataOutType": "Step Speed Progress PotentialEnergy Temperature Time Volume"}
680 else:
681 ParamsDefaultInfoOverride = {"DataOutType": "Step Speed Progress PotentialEnergy Temperature Time Density"}
682 OptionsInfo["OutputParams"] = OpenMMUtil.ProcessOptionOpenMMOutputParameters("--outputParams", Options["--outputParams"], OptionsInfo["OutfilePrefix"], ParamsDefaultInfoOverride)
683 ProcessOutfileNames()
684
685 OptionsInfo["ForcefieldParams"] = OpenMMUtil.ProcessOptionOpenMMForcefieldParameters("--forcefieldParams", Options["--forcefieldParams"])
686
687 OptionsInfo["FreezeAtoms"] = True if re.match("^yes$", Options["--freezeAtoms"], re.I) else False
688 if OptionsInfo["FreezeAtoms"]:
689 OptionsInfo["FreezeAtomsParams"] = OpenMMUtil.ProcessOptionOpenMMAtomsSelectionParameters("--freezeAtomsParams", Options["--freezeAtomsParams"])
690 else:
691 OptionsInfo["FreezeAtomsParams"] = None
692
693 ParamsDefaultInfoOverride = {"Name": Options["--platform"], "Threads": 1}
694 OptionsInfo["PlatformParams"] = OpenMMUtil.ProcessOptionOpenMMPlatformParameters("--platformParams", Options["--platformParams"], ParamsDefaultInfoOverride)
695
696 OptionsInfo["RestraintAtoms"] = True if re.match("^yes$", Options["--restraintAtoms"], re.I) else False
697 if OptionsInfo["RestraintAtoms"]:
698 OptionsInfo["RestraintAtomsParams"] = OpenMMUtil.ProcessOptionOpenMMAtomsSelectionParameters("--restraintAtomsParams", Options["--restraintAtomsParams"])
699 else:
700 OptionsInfo["RestraintAtomsParams"] = None
701 OptionsInfo["RestraintSpringConstant"] = float(Options["--restraintSpringConstant"])
702
703 ProcessRestartParameters()
704
705 OptionsInfo["SystemParams"] = OpenMMUtil.ProcessOptionOpenMMSystemParameters("--systemParams", Options["--systemParams"])
706
707 OptionsInfo["IntegratorParams"] = OpenMMUtil.ProcessOptionOpenMMIntegratorParameters("--integratorParams", Options["--integratorParams"], HydrogenMassRepartioningStatus = OptionsInfo["SystemParams"]["HydrogenMassRepartioning"])
708
709 OptionsInfo["SimulationParams"] = OpenMMUtil.ProcessOptionOpenMMSimulationParameters("--simulationParams", Options["--simulationParams"])
710
711 ProcessWaterBoxParameters()
712
713 OptionsInfo["Overwrite"] = Options["--overwrite"]
714
715 def RetrieveOptions():
716 """Retrieve command line arguments and options."""
717
718 # Get options...
719 global Options
720 Options = docopt(_docoptUsage_)
721
722 # Set current working directory to the specified directory...
723 WorkingDir = Options["--workingdir"]
724 if WorkingDir:
725 os.chdir(WorkingDir)
726
727 # Handle examples option...
728 if "--examples" in Options and Options["--examples"]:
729 MiscUtil.PrintInfo(MiscUtil.GetExamplesTextFromDocOptText(_docoptUsage_))
730 sys.exit(0)
731
732 def ValidateOptions():
733 """Validate option values."""
734
735 MiscUtil.ValidateOptionFilePath("-i, --infile", Options["--infile"])
736 MiscUtil.ValidateOptionFileExt("-i, --infile", Options["--infile"], "pdb cif")
737
738 FileDir, FileName, FileExt = MiscUtil.ParseFileName(Options["--infile"])
739 OutfilePrefix = Options["--outfilePrefix"]
740 if not re.match("^auto$", OutfilePrefix, re.I):
741 if re.match("^(%s)$" % OutfilePrefix, FileName, re.I):
742 MiscUtil.PrintError("The value specified, %s, for option \"--outfilePrefix\" is not valid. You must specify a value different from, %s, the root of infile name." % (OutfilePrefix, FileName))
743
744 if Options["--smallMolFile"] is not None:
745 MiscUtil.ValidateOptionFilePath("-l, --smallMolFile", Options["--smallMolFile"])
746 MiscUtil.ValidateOptionFileExt("-l, --smallMolFile", Options["--smallMolFile"], "sd sdf")
747
748 SmallMolID = Options["--smallMolID"]
749 if len(SmallMolID) != 3:
750 MiscUtil.PrintError("The value specified, %s, for option \"--smallMolID\" is not valid. You must specify a three letter small molecule ID." % (SmallMolID))
751
752 MiscUtil.ValidateOptionTextValue("--freezeAtoms", Options["--freezeAtoms"], "yes no")
753 if re.match("^yes$", Options["--freezeAtoms"], re.I):
754 if Options["--freezeAtomsParams"] is None:
755 MiscUtil.PrintError("No value specified for option \"--freezeAtomsParams\". You must specify valid values during, yes, value for \"--freezeAtoms\" option.")
756
757 MiscUtil.ValidateOptionTextValue("-m, --mode", Options["--mode"], "NPT NVT")
758
759 MiscUtil.ValidateOptionTextValue("-p, --platform", Options["--platform"], "CPU CUDA OpenCL Reference")
760
761 MiscUtil.ValidateOptionTextValue("-r, --restart ", Options["--restart"], "yes no")
762
763 MiscUtil.ValidateOptionTextValue("--restraintAtoms", Options["--restraintAtoms"], "yes no")
764 if re.match("^yes$", Options["--restraintAtoms"], re.I):
765 if Options["--restraintAtomsParams"] is None:
766 MiscUtil.PrintError("No value specified for option \"--restraintAtomsParams\". You must specify valid values during, yes, value for \"--restraintAtoms\" option.")
767
768 MiscUtil.ValidateOptionFloatValue("--restraintSpringConstant", Options["--restraintSpringConstant"], {">": 0})
769
770 MiscUtil.ValidateOptionTextValue("--waterBox", Options["--waterBox"], "yes no")
771
772 # Setup a usage string for docopt...
773 _docoptUsage_ = """
774 OpenMMPerformMDSimulation.py - Perform a MD simulation.
775
776 Usage:
777 OpenMMPerformMDSimulation.py [--forcefieldParams <Name,Value,..>] [--freezeAtoms <yes or no>]
778 [--freezeAtomsParams <Name,Value,..>] [--integratorParams <Name,Value,..>]
779 [--mode <NVT or NPT>] [--outputParams <Name,Value,..>] [--outfilePrefix <text>]
780 [--overwrite] [--platform <text>] [--platformParams <Name,Value,..>] [--restart <yes or no>]
781 [--restartParams <Name,Value,..>] [--restraintAtoms <yes or no>]
782 [--restraintAtomsParams <Name,Value,..>] [--restraintSpringConstant <number>]
783 [--simulationParams <Name,Value,..>] [--smallMolFile <SmallMolFile>] [--smallMolID <text>]
784 [--systemParams <Name,Value,..>] [--waterBox <yes or no>]
785 [--waterBoxParams <Name,Value,..>] [-w <dir>] -i <infile>
786 OpenMMPerformMDSimulation.py -h | --help | -e | --examples
787
788 Description:
789 Perform a MD simulation using an NPT or NVT statistical ensemble. You may
790 run a simulation using a macromolecule or a macromolecule in a complex with
791 small molecule. By default, the system is minimized and equilibrated before the
792 production run.
793
794 The input file must contain a macromolecule already prepared for simulation.
795 The preparation of the macromolecule for a simulation generally involves the
796 following: tasks: Identification and replacement non-standard residues;
797 Addition of missing residues; Addition of missing heavy atoms; Addition of
798 missing hydrogens; Addition of a water box which is optional.
799
800 In addition, the small molecule input file must contain a molecule already
801 prepared for simulation. It must contain appropriate 3D coordinates relative
802 to the macromolecule along with no missing hydrogens.
803
804 You may optionally add a water box and freeze/restraint atoms for the
805 simulation.
806
807 The supported macromolecule input file formats are: PDB (.pdb) and
808 CIF (.cif)
809
810 The supported small molecule input file format are : SD (.sdf, .sd)
811
812 Possible outfile prefixes:
813
814 <InfieRoot>_<Mode>
815 <InfieRoot>_Solvated_<Mode>
816 <InfieRoot>_<SmallMolFileRoot>_Complex_<Mode>,
817 <InfieRoot>_<SmallMolFileRoot>_Complex_Solvated_<Mode>
818
819 Possible output files:
820
821 <OutfilePrefix>.<pdb or cif> [ Initial sytem ]
822 <OutfilePrefix>.<dcd or xtc>
823
824 <OutfilePrefix>_Reimaged.<pdb or cif> [ First frame ]
825 <OutfilePrefix>_Reimaged.<dcd or xtc>
826
827 <OutfilePrefix>_Minimized.<pdb or cif>
828 <OutfilePrefix>_Equilibrated.<pdb or cif>
829 <OutfilePrefix>_Final.<pdb or cif> [ Final system ]
830
831 <OutfilePrefix>.chk
832 <OutfilePrefix>.csv
833 <OutfilePrefix>_Minimization.csv
834 <OutfilePrefix>_FinalState.chk
835 <OutfilePrefix>_FinalState.xml
836
837 <OutfilePrefix>_System.xml
838 <OutfilePrefix>_Integrator.xml
839
840 The reimaged PDB file, <OutfilePrefix>_Reimaged.pdb, corresponds to the first
841 frame in the trajectory. The reimaged trajectory file contains all the frames
842 aligned to the first frame after reimaging of the frames for periodic systems.
843
844 Options:
845 -e, --examples
846 Print examples.
847 -f, --forcefieldParams <Name,Value,..> [default: auto]
848 A comma delimited list of parameter name and value pairs for biopolymer,
849 water, and small molecule forcefields.
850
851 The supported parameter names along with their default values are
852 are shown below:
853
854 biopolymer, amber14-all.xml [ Possible values: Any Valid value ]
855 smallMolecule, openff-2.2.1 [ Possible values: Any Valid value ]
856 water, auto [ Possible values: Any Valid value ]
857 additional, none [ Possible values: Space delimited list of any
858 valid value ]
859
860 Possible biopolymer forcefield values:
861
862 amber14-all.xml, amber99sb.xml, amber99sbildn.xml, amber03.xml,
863 amber10.xml
864 charmm36.xml, charmm_polar_2019.xml
865 amoeba2018.xml
866
867 Possible small molecule forcefield values:
868
869 openff-2.2.1, openff-2.0.0, openff-1.3.1, openff-1.2.1,
870 openff-1.1.1, openff-1.1.0,...
871 smirnoff99Frosst-1.1.0, smirnoff99Frosst-1.0.9,...
872 gaff-2.11, gaff-2.1, gaff-1.81, gaff-1.8, gaff-1.4,...
873
874 The default water forcefield valus is dependent on the type of the
875 biopolymer forcefield as shown below:
876
877 Amber: amber14/tip3pfb.xml
878 CHARMM: charmm36/water.xml or None for charmm_polar_2019.xml
879 Amoeba: None (Explicit)
880
881 Possible water forcefield values:
882
883 amber14/tip3p.xml, amber14/tip3pfb.xml, amber14/spce.xml,
884 amber14/tip4pew.xml, amber14/tip4pfb.xml,
885 charmm36/water.xml, charmm36/tip3p-pme-b.xml,
886 charmm36/tip3p-pme-f.xml, charmm36/spce.xml,
887 charmm36/tip4pew.xml, charmm36/tip4p2005.xml,
888 charmm36/tip5p.xml, charmm36/tip5pew.xml,
889 implicit/obc2.xml, implicit/GBn.xml, implicit/GBn2.xml,
890 amoeba2018_gk.xml (Implict water)
891 None (Explicit water for amoeba)
892
893 The additional forcefield value is a space delimited list of any valid
894 forcefield values and is passed on to the OpenMMForcefields
895 SystemGenerator along with the specified forcefield values for
896 biopolymer, water, and mall molecule. Possible additional forcefield
897 values are:
898
899 amber14/DNA.OL15.xml amber14/RNA.OL3.xml
900 amber14/lipid17.xml amber14/GLYCAM_06j-1.xml
901 ... ... ...
902
903 You may specify any valid forcefield names supported by OpenMM. No
904 explicit validation is performed.
905 --freezeAtoms <yes or no> [default: no]
906 Freeze atoms during a simulation. The specified atoms are kept completely
907 fixed by setting their masses to zero. Their positions do not change during
908 local energy minimization and MD simulation, and they do not contribute
909 to the kinetic energy of the system.
910 --freezeAtomsParams <Name,Value,..>
911 A comma delimited list of parameter name and value pairs for freezing
912 atoms during a simulation. You must specify these parameters for 'yes'
913 value of '--freezeAtoms' option.
914
915 The supported parameter names along with their default values are
916 are shown below:
917
918 selection, none [ Possible values: CAlphaProtein, Ions, Ligand,
919 Protein, Residues, or Water ]
920 selectionSpec, auto [ Possible values: A space delimited list of
921 residue names ]
922 negate, no [ Possible values: yes or no ]
923
924 A brief description of parameters is provided below:
925
926 selection: Atom selection to freeze.
927 selectionSpec: A space delimited list of residue names for
928 selecting atoms to freeze. You must specify its value during
929 'Ligand' and 'Protein' value for 'selection'. The default values
930 are automatically set for 'CAlphaProtein', 'Ions', 'Protein',
931 and 'Water' values of 'selection' as shown below:
932
933 CAlphaProtein: List of stadard protein residues from pdbfixer
934 for selecting CAlpha atoms.
935 Ions: Li Na K Rb Cs Cl Br F I
936 Water: HOH
937 Protein: List of standard protein residues from pdbfixer.
938
939 negate: Negate atom selection match to select atoms for freezing.
940
941 In addition, you may specify an explicit space delimited list of residue
942 names using 'selectionSpec' for any 'selection". The specified residue
943 names are appended to the appropriate default values during the
944 selection of atoms for freezing.
945 -h, --help
946 Print this help message.
947 -i, --infile <infile>
948 Input file name containing a macromolecule.
949 --integratorParams <Name,Value,..> [default: auto]
950 A comma delimited list of parameter name and value pairs for integrator
951 during a simulation.
952
953 The supported parameter names along with their default values are
954 are shown below:
955
956 integrator, LangevinMiddle [ Possible values: LangevinMiddle,
957 Langevin, NoseHoover, Brownian ]
958
959 randomSeed, auto [ Possible values: > 0 ]
960
961 frictionCoefficient, 1.0 [ Units: 1/ps ]
962 stepSize, auto [ Units: fs; Default value: 4 fs during yes value of
963 hydrogen mass repartioning with no freezing/restraining of atoms;
964 otherwsie, 2 fs ]
965 temperature, 300.0 [ Units: kelvin ]
966
967 barostat, MonteCarlo [ Possible values: MonteCarlo or
968 MonteCarloMembrane ]
969 barostatInterval, 25
970 pressure, 1.0 [ Units: atm ]
971
972 Parameters used only for MonteCarloMembraneBarostat with default
973 values corresponding to Amber forcefields:
974
975 surfaceTension, 0.0 [ Units: atm*A. It is automatically converted
976 into OpenMM default units of atm*nm before its usage. ]
977 xymode, Isotropic [ Possible values: Anisotropic or Isotropic ]
978 zmode, Free [ Possible values: Free or Fixed ]
979
980 A brief description of parameters is provided below:
981
982 integrator: Type of integrator
983
984 randomSeed: Random number seed for barostat and integrator. Not
985 supported for NoseHoover integrator.
986
987 frictionCoefficient: Friction coefficient for coupling the system to
988 the heat bath..
989 stepSize: Simulation time step size.
990 temperature: Simulation temperature.
991
992 barostat: Barostat type.
993 barostatInterval: Barostat interval step size during NPT
994 simulation for applying Monte Carlo pressure changes.
995 pressure: Pressure during NPT simulation.
996
997 Parameters used only for MonteCarloMembraneBarostat:
998
999 surfaceTension: Surface tension acting on the system.
1000 xymode: Behavior along X and Y axes. You may allow the X and Y axes
1001 to vary independently of each other or always scale them by the same
1002 amount to keep the ratio of their lengths constant.
1003 zmode: Beahvior along Z axis. You may allow the Z axis to vary
1004 independently of the other axes or keep it fixed.
1005
1006 -m, --mode <NPT or NVT> [default: NPT]
1007 Type of statistical ensemble to use for simulation. Possible values:
1008 NPT (constant Number of particles, Pressure, and Temperature) or
1009 NVT ((constant Number of particles, Volume and Temperature)
1010 --outfilePrefix <text> [default: auto]
1011 File prefix for generating the names of output files. The default value
1012 depends on the names of input files for macromolecule and small molecule
1013 along with the type of statistical ensemble and the nature of the solvation.
1014
1015 The possible values for outfile prefix are shown below:
1016
1017 <InfieRoot>_<Mode>
1018 <InfieRoot>_Solvated_<Mode>
1019 <InfieRoot>_<SmallMolFileRoot>_Complex_<Mode>,
1020 <InfieRoot>_<SmallMolFileRoot>_Complex_Solvated_<Mode>
1021
1022 --outputParams <Name,Value,..> [default: auto]
1023 A comma delimited list of parameter name and value pairs for generating
1024 output during a simulation.
1025
1026 The supported parameter names along with their default values are
1027 are shown below:
1028
1029 checkpoint, no [ Possible values: yes or no ]
1030 checkpointFile, auto [ Default: <OutfilePrefix>.chk ]
1031 checkpointSteps, 10000
1032
1033 dataOutType, auto [ Possible values: A space delimited list of valid
1034 parameter names.
1035 NPT simulation default: Density Step Speed Progress
1036 PotentialEnergy Temperature Time.
1037 NVT simulation default: Step Speed Progress PotentialEnergy
1038 Temperature Time Volumne
1039 Other valid names: ElapsedTime RemainingTime KineticEnergy
1040 TotalEnergy ]
1041
1042 dataLog, yes [ Possible values: yes or no ]
1043 dataLogFile, auto [ Default: <OutfilePrefix>.csv ]
1044 dataLogSteps, 1000
1045
1046 dataStdout, no [ Possible values: yes or no ]
1047 dataStdoutSteps, 1000
1048
1049 minimizationDataSteps, 100
1050 minimizationDataStdout, no [ Possible values: yes or no ]
1051 minimizationDataLog, no [ Possible values: yes or no ]
1052 minimizationDataLogFile, auto [ Default:
1053 <OutfilePrefix>_MinimizationOut.csv ]
1054 minimizationDataOutType, auto [ Possible values: A space delimited
1055 list of valid parameter names. Default: SystemEnergy
1056 RestraintEnergy MaxConstraintError.
1057 Other valid names: RestraintStrength ]
1058
1059 pdbOutFormat, PDB [ Possible values: PDB or CIF ]
1060 pdbOutKeepIDs, yes [ Possible values: yes or no ]
1061
1062 pdbOutMinimized, no [ Possible values: yes or no ]
1063 pdbOutEquilibrated, no [ Possible values: yes or no ]
1064 pdbOutFinal, no [ Possible values: yes or no ]
1065
1066 saveFinalStateCheckpoint, yes [ Possible values: yes or no ]
1067 saveFinalStateCheckpointFile, auto [ Default:
1068 <OutfilePrefix>_FinalState.chk ]
1069 saveFinalStateXML, no [ Possible values: yes or no ]
1070 saveFinalStateXMLFile, auto [ Default:
1071 <OutfilePrefix>_FinalState.xml]
1072
1073 traj, yes [ Possible values: yes or no ]
1074 trajFile, auto [ Default: <OutfilePrefix>.<TrajFormat> ]
1075 trajFormat, DCD [ Possible values: DCD or XTC ]
1076 trajSteps, 10000 [ The default value corresponds to 40 ps for step
1077 size of 4 fs. ]
1078
1079 xmlSystemOut, no [ Possible values: yes or no ]
1080 xmlSystemFile, auto [ Default: <OutfilePrefix>_System.xml ]
1081 xmlIntegratorOut, no [ Possible values: yes or no ]
1082 xmlIntegratorFile, auto [ Default: <OutfilePrefix>_Integrator.xml ]
1083
1084 A brief description of parameters is provided below:
1085
1086 checkpoint: Write intermediate checkpoint file.
1087 checkpointFile: Intermediate checkpoint file name.
1088 checkpointSteps: Frequency of writing intermediate checkpoint file.
1089
1090 dataOutType: Type of data to write to stdout and log file.
1091
1092 dataLog: Write data to log file.
1093 dataLogFile: Data log file name.
1094 dataLogSteps: Frequency of writing data to log file.
1095
1096 dataStdout: Write data to stdout.
1097 dataStdoutSteps: Frequency of writing data to stdout.
1098
1099 minimizationDataSteps: Frequency of writing data to stdout
1100 and log file.
1101 minimizationDataStdout: Write data to stdout.
1102 minimizationDataLog: Write data to log file.
1103 minimizationDataLogFile: Data log fie name.
1104 minimizationDataOutType: Type of data to write to stdout
1105 and log file.
1106
1107 saveFinalStateCheckpoint: Save final state checkpoint file.
1108 saveFinalStateCheckpointFile: Name of final state checkpoint file.
1109 saveFinalStateXML: Save final state XML file.
1110 saveFinalStateXMLFile: Name of final state XML file.
1111
1112 pdbOutFormat: Format of output PDB files.
1113 pdbOutKeepIDs: Keep existing chain and residue IDs.
1114
1115 pdbOutMinimized: Write PDB file after minimization.
1116 pdbOutEquilibrated: Write PDB file after equilibration.
1117 pdbOutFinal: Write final PDB file after production run.
1118
1119 traj: Write out trajectory file.
1120 trajFile: Trajectory file name.
1121 trajFormat: Trajectory file format.
1122 trajSteps: Frequency of writing trajectory file.
1123
1124 xmlSystemOut: Write system XML file.
1125 xmlSystemFile: System XML file name.
1126 xmlIntegratorOut: Write integrator XML file.
1127 xmlIntegratorFile: Integrator XML file name.
1128
1129 --overwrite
1130 Overwrite existing files.
1131 -p, --platform <text> [default: CPU]
1132 Platform to use for running MD simulation. Possible values: CPU, CUDA,
1133 OpenCL, or Reference.
1134 --platformParams <Name,Value,..> [default: auto]
1135 A comma delimited list of parameter name and value pairs to configure
1136 platform for running MD simulation.
1137
1138 The supported parameter names along with their default values for
1139 different platforms are shown below:
1140
1141 CPU:
1142
1143 threads, 1 [ Possible value: >= 0 or auto. The value of 'auto'
1144 or zero implies the use of all available CPUs for threading. ]
1145
1146 CUDA:
1147
1148 deviceIndex, auto [ Possible values: 0, '0 1' etc. ]
1149 deterministicForces, auto [ Possible values: yes or no ]
1150 precision, single [ Possible values: single, double, or mix ]
1151 tempDirectory, auto [ Possible value: DirName ]
1152 useBlockingSync, auto [ Possible values: yes or no ]
1153 useCpuPme, auto [ Possible values: yes or no ]
1154
1155 OpenCL:
1156
1157 deviceIndex, auto [ Possible values: 0, '0 1' etc. ]
1158 openCLPlatformIndex, auto [ Possible value: Number]
1159 precision, single [ Possible values: single, double, or mix ]
1160 useCpuPme, auto [ Possible values: yes or no ]
1161
1162 A brief description of parameters is provided below:
1163
1164 CPU:
1165
1166 threads: Number of threads to use for simulation.
1167
1168 CUDA:
1169
1170 deviceIndex: Space delimited list of device indices to use for
1171 calculations.
1172 deterministicForces: Generate reproducible results at the cost of a
1173 small decrease in performance.
1174 precision: Number precision to use for calculations.
1175 tempDirectory: Directory name for storing temporary files.
1176 useBlockingSync: Control run-time synchronization between CPU and
1177 GPU.
1178 useCpuPme: Use CPU-based PME implementation.
1179
1180 OpenCL:
1181
1182 deviceIndex: Space delimited list of device indices to use for
1183 simulation.
1184 openCLPlatformIndex: Platform index to use for calculations.
1185 precision: Number precision to use for calculations.
1186 useCpuPme: Use CPU-based PME implementation.
1187
1188 -r, --restart <yes or no> [default: no]
1189 Restart simulation using a previously saved final state checkpoint or
1190 XML file.
1191 --restartParams <Name,Value,..> [default: auto]
1192 A comma delimited list of parameter name and value pairs for restarting
1193 a simulation.
1194
1195 The supported parameter names along with their default values are
1196 are shown below:
1197
1198 finalStateFile, <OutfilePrefix>_FinalState.<chk> [ Possible values:
1199 Valid final state checkpoint or XML filename ]
1200 dataAppend, yes [ Possible values: yes or no]
1201
1202 A brief description of parameters is provided below:
1203
1204 finalStateFile: Final state checkpoint or XML file
1205 dataAppend: Append data to existing trajectory and data log files
1206 during the restart of a simulation using a previously saved final
1207 state checkpoint or XML file.
1208
1209 --restraintAtoms <yes or no> [default: no]
1210 Restraint atoms during a simulation. The motion of specified atoms is
1211 restricted by adding a harmonic force that binds them to their starting
1212 positions. The atoms are not completely fixed unlike freezing of atoms.
1213 Their motion, however, is restricted and they are not able to move far away
1214 from their starting positions during local energy minimization and MD
1215 simulation.
1216 --restraintAtomsParams <Name,Value,..>
1217 A comma delimited list of parameter name and value pairs for restraining
1218 atoms during a simulation. You must specify these parameters for 'yes'
1219 value of '--restraintAtoms' option.
1220
1221 The supported parameter names along with their default values are
1222 are shown below:
1223
1224 selection, none [ Possible values: CAlphaProtein, Ions, Ligand,
1225 Protein, Residues, or Water ]
1226 selectionSpec, auto [ Possible values: A space delimited list of
1227 residue names ]
1228 negate, no [ Possible values: yes or no ]
1229
1230 A brief description of parameters is provided below:
1231
1232 selection: Atom selection to restraint.
1233 selectionSpec: A space delimited list of residue names for
1234 selecting atoms to restraint. You must specify its value during
1235 'Ligand' and 'Protein' value for 'selection'. The default values
1236 are automatically set for 'CAlphaProtein', 'Ions', 'Protein',
1237 and 'Water' values of 'selection' as shown below:
1238
1239 CAlphaProtein: List of stadard protein residues from pdbfixer
1240 for selecting CAlpha atoms.
1241 Ions: Li Na K Rb Cs Cl Br F I
1242 Water: HOH
1243 Protein: List of standard protein residues from pdbfixer.
1244
1245 negate: Negate atom selection match to select atoms for freezing.
1246
1247 In addition, you may specify an explicit space delimited list of residue
1248 names using 'selectionSpec' for any 'selection". The specified residue
1249 names are appended to the appropriate default values during the
1250 selection of atoms for restraining.
1251 --restraintSpringConstant <number> [default: 2.5]
1252 Restraint spring constant for applying external restraint force to restraint
1253 atoms relative to their initial positions during 'yes' value of '--restraintAtoms'
1254 option. Default units: kcal/mol/A**2. The default value, 2.5, corresponds to
1255 1046.0 kjoules/mol/nm**2. The default value is automatically converted into
1256 units of kjoules/mol/nm**2 before its usage.
1257 --simulationParams <Name,Value,..> [default: auto]
1258 A comma delimited list of parameter name and value pairs for simulation.
1259
1260 The supported parameter names along with their default values are
1261 are shown below:
1262
1263 steps, 1000000 [ Possible values: > 0. The default value
1264 corresponds to 4 ns for step size of 4 fs. ]
1265
1266 minimization, yes [ Possible values: yes or no ]
1267 minimizationMaxSteps, auto [ Possible values: >= 0. The value of
1268 zero implies until the minimization is converged. ]
1269 minimizationTolerance, 0.24 [ Units: kcal/mol/A. The default value
1270 0.25, corresponds to OpenMM default of value of 10.04
1271 kjoules/mol/nm. It is automatically converted into OpenMM
1272 default units before its usage. ]
1273
1274 equilibration, yes [ Possible values: yes or no ]
1275 equilibrationSteps, 1000 [ Possible values: > 0 ]
1276
1277 A brief description of parameters is provided below:
1278
1279 steps: Number of steps for production run.
1280
1281 minimization: Perform minimization before equilibration and
1282 production run.
1283 minimizationMaxSteps: Maximum number of minimization steps. The
1284 value of zero implies until the minimization is converged.
1285 minimizationTolerance: Energy convergence tolerance during
1286 minimization.
1287
1288 equilibration: Perform equilibration before the production run.
1289 equilibrationSteps: Number of steps for equilibration.
1290
1291 -s, --smallMolFile <SmallMolFile>
1292 Small molecule input file name. The macromolecue and small molecule are
1293 merged for simulation and the complex is written out to a PDB file.
1294 --smallMolID <text> [default: LIG]
1295 Three letter small molecule residue ID. The small molecule ID corresponds
1296 to the residue name of the small molecule and is written out to a PDB file
1297 containing the complex.
1298 --systemParams <Name,Value,..> [default: auto]
1299 A comma delimited list of parameter name and value pairs to configure
1300 a system for simulation.
1301
1302 The supported parameter names along with their default values are
1303 are shown below:
1304
1305 constraints, BondsInvolvingHydrogens [ Possible values: None,
1306 WaterOnly, BondsInvolvingHydrogens, AllBonds, or
1307 AnglesInvolvingHydrogens ]
1308 constraintErrorTolerance, 0.000001
1309 ewaldErrorTolerance, 0.0005
1310
1311 nonbondedMethodPeriodic, PME [ Possible values: NoCutoff,
1312 CutoffNonPeriodic, or PME ]
1313 nonbondedMethodNonPeriodic, NoCutoff [ Possible values:
1314 NoCutoff or CutoffNonPeriodic]
1315 nonbondedCutoff, 1.0 [ Units: nm ]
1316
1317 hydrogenMassRepartioning, yes [ Possible values: yes or no ]
1318 hydrogenMass, 1.5 [ Units: amu]
1319
1320 removeCMMotion, yes [ Possible values: yes or no ]
1321 rigidWater, auto [ Possible values: yes or no. Default: 'No' for
1322 'None' value of constraints; Otherwise, yes ]
1323
1324 A brief description of parameters is provided below:
1325
1326 constraints: Type of system constraints to use for simulation. These
1327 constraints are different from freezing and restraining of any
1328 atoms in the system.
1329 constraintErrorTolerance: Distance tolerance for constraints as a
1330 fraction of the constrained distance.
1331 ewaldErrorTolerance: Ewald error tolerance for a periodic system.
1332
1333 nonbondedMethodPeriodic: Nonbonded method to use during the
1334 calculation of long range interactions for a periodic system.
1335 nonbondedMethodNonPeriodic: Nonbonded method to use during the
1336 calculation of long range interactions for a non-periodic system.
1337 nonbondedCutoff: Cutoff distance to use for long range interactions
1338 in both perioidic non-periodic systems.
1339
1340 hydrogenMassRepartioning: Use hydrogen mass repartioning. It
1341 increases the mass of the hydrogen atoms attached to the heavy
1342 atoms and decreasing the mass of the bonded heavy atom to
1343 maintain constant system mass. This allows the use of larger
1344 integration step size (4 fs) during a simulation.
1345 hydrogenMass: Hydrogen mass to use during repartioning.
1346
1347 removeCMMotion: Remove all center of mass motion at every time step.
1348 rigidWater: Keep water rigid during a simulation. This is determined
1349 automatically based on the value of 'constraints' parameter.
1350
1351 --waterBox <yes or no> [default: no]
1352 Add water box.
1353 --waterBoxParams <Name,Value,..> [default: auto]
1354 A comma delimited list of parameter name and value pairs for adding
1355 a water box.
1356
1357 The supported parameter names along with their default values are
1358 are shown below:
1359
1360 model, tip3p [ Possible values: tip3p, spce, tip4pew, tip5p or
1361 swm4ndp ]
1362 mode, Padding [ Possible values: Size or Padding ]
1363 padding, 1.0
1364 size, None [ Possible value: xsize ysize zsize ]
1365 shape, cube [ Possible values: cube, dodecahedron, or octahedron ]
1366 ionPositive, Na+ [ Possible values: Li+, Na+, K+, Rb+, or Cs+ ]
1367 ionNegative, Cl- [ Possible values: Cl-, Br-, F-, or I- ]
1368 ionicStrength, 0.0
1369
1370 A brief description of parameters is provided below:
1371
1372 model: Water model to use for adding water box. The van der
1373 Waals radii and atomic charges are determined using the
1374 specified water forcefield. You must specify an appropriate
1375 water forcefield. No validation is performed.
1376 mode: Specify the size of the waterbox explicitly or calculate it
1377 automatically for a macromolecule along with adding padding
1378 around ther macromolecule.
1379 padding: Padding around a macromolecule in nanometers for filling
1380 box with water. It must be specified during 'Padding' value of
1381 'mode' parameter.
1382 size: A space delimited triplet of values corresponding to water
1383 size in nanometers. It must be specified during 'Size' value of
1384 'mode' parameter.
1385 ionPositive: Type of positive ion to add during the addition of a
1386 water box.
1387 ionNegative: Type of negative ion to add during the addition of a
1388 water box.
1389 ionicStrength: Total concentration of both positive and negative
1390 ions to add excluding the ions added to neutralize the system
1391 during the addition of a water box.
1392
1393 -w, --workingdir <dir>
1394 Location of working directory which defaults to the current directory.
1395
1396 Examples:
1397 To perform a MD simulation for a macromolecule in a PDB file by using an NPT
1398 ensemble, applying system constraints for bonds involving hydrogens along
1399 with hydrogen mass repartioning, using a step size of 4 fs, performing minimization
1400 until it's converged along with equilibration for 1,000 steps ( 4 ps), performing
1401 production run for 1,000,000 steps (4 ns), writing trajectory file every 10,000
1402 steps (40 ps), writing data log file every 1,000 steps (4 ps), generating a checkpoint
1403 file after the completion of the, and generating a PDB for the final system, type:
1404
1405 % OpenMMPerformMDSimulation.py -i Sample13.pdb --waterBox yes
1406
1407 To run the first example for performing OpenMM simulation using multi-
1408 threading employing all available CPUs on your machine and generate various
1409 output files, type:
1410
1411 % OpenMMPerformMDSimulation.py -i Sample13.pdb --waterBox yes
1412 --platformParams "threads,0"
1413
1414 To run the first example for performing OpenMM simulation using CUDA platform
1415 on your machine and generate various output files, type:
1416
1417 % OpenMMPerformMDSimulation.py -i Sample13.pdb --waterBox yes -p CUDA
1418
1419 To run the second example for a marcomolecule in a complex with a small
1420 molecule and generate various output files, type:
1421
1422 % OpenMMPerformMDSimulation.py -i Sample13.pdb -s Sample13Ligand.sdf
1423 --waterBox yes --platformParams "threads,0"
1424
1425 To run the second example for performing NVT simulation and generate various
1426 output files, type:
1427
1428 % OpenMMPerformMDSimulation.py -i Sample13.pdb -s Sample13Ligand.sdf
1429 --mode NVT --platformParams "threads,0"
1430
1431 % OpenMMPerformMDSimulation.py -i Sample13.pdb -s Sample13Ligand.sdf
1432 --mode NVT --waterBox yes --platformParams "threads,0"
1433
1434 To run the second example for a macromolecule in a lipid bilayer, write out
1435 reimaged and realigned trajectory file for the periodic system, along with a
1436 PDB file corresponding to the first frame, and generate various output files,
1437 type:
1438
1439 % OpenMMPerformMDSimulation.py -i Sample12LipidBilayer.pdb
1440 --platformParams "threads,0" --integratorParams
1441 "barostat,MonteCarloMembrane"
1442
1443 To run the second example by freezing CAlpha atoms in a macromolecule without
1444 using any system constraints to avoid any issues with the freezing of the same atoms,
1445 using a step size of 2 fs, and generate various output files, type:
1446
1447 % OpenMMPerformMDSimulation.py -i Sample13.pdb --waterBox yes
1448 --freezeAtoms yes --freezeAtomsParams "selection,CAlphaProtein"
1449 --systemParams "constraints, None"
1450 --platformParams "threads,0" --integratorParams "stepSize,2"
1451
1452 To run the second example by restrainting CAlpha atoms in a macromolecule and
1453 and generate various output files, type:
1454
1455 % OpenMMPerformMDSimulation.py -i Sample13.pdb --waterBox yes
1456 --restraintAtomsParams "selection,CAlphaProtein"
1457 --platformParams "threads,0" --integratorParams "stepSize,2"
1458
1459 To run the second example for a marcomolecule in a complex with a small
1460 molecule by using implicit water and generate various output files, type:
1461
1462 % OpenMMPerformMDSimulation.py -i Sample13.pdb -s Sample13Ligand.sdf
1463 --mode NVT --platformParams "threads,0"
1464 --forcefieldParams "biopolymer, amber14-all.xml, water,
1465 implicit/obc2.xml"
1466
1467 To run the second example by specifying explict values for various parametres
1468 and generate various output files, type:
1469
1470 % OpenMMPerformMDSimulation.py -m NPT -i Sample13.pdb
1471 -f " biopolymer,amber14-all.xml,smallMolecule, openff-2.2.1,
1472 water,amber14/tip3pfb.xml" --waterBox yes
1473 --integratorParams "integrator,LangevinMiddle,randomSeed,42,
1474 stepSize,2, temperature, 300.0,pressure, 1.0"
1475 --outputParams "checkpoint,yes,dataLog,yes,dataStdout,yes,
1476 minimizationDataStdout,yes,minimizationDataLog,yes,
1477 pdbOutFormat,CIF,pdbOutKeepIDs,yes,saveFinalStateCheckpoint, yes,
1478 traj,yes,xmlSystemOut,yes,xmlIntegratorOut,yes"
1479 -p CPU --platformParams "threads,0"
1480 --simulationParams "steps,10000,minimization,yes,
1481 minimizationMaxSteps,500,equilibration,yes,equilibrationSteps,1000"
1482 --systemParams "constraints,BondsInvolvingHydrogens,
1483 nonbondedMethodPeriodic,PME,nonbondedMethodNonPeriodic,NoCutoff,
1484 hydrogenMassRepartioning, yes"
1485
1486 Author:
1487 Manish Sud(msud@san.rr.com)
1488
1489 See also:
1490 OpenMMPrepareMacromolecule.py, OpenMMPerformMinimization.py
1491
1492 Copyright:
1493 Copyright (C) 2025 Manish Sud. All rights reserved.
1494
1495 The functionality available in this script is implemented using OpenMM, an
1496 open source molecuar simulation package.
1497
1498 This file is part of MayaChemTools.
1499
1500 MayaChemTools is free software; you can redistribute it and/or modify it under
1501 the terms of the GNU Lesser General Public License as published by the Free
1502 Software Foundation; either version 3 of the License, or (at your option) any
1503 later version.
1504
1505 """
1506
1507 if __name__ == "__main__":
1508 main()
