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https://github.com/openmm/openmm
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939e0af545
* Add basic version of TinkerFiles * Refactor TinkerFiles * Update docstring, type hints, and fix bug when setting box vectors * Small fixes * Add unit tests for the TinkerFiles class * Fixes and updates to TinkerFiles * Add simuteTinker example * Update Modeller to work with AMOEBA force fields * Small fixes * Relax type hinting * Fix indices in modeller * Fix modeller indices * Fix type hints and usage of Quantity * Remove numpy protector * Add reader of .seq files * Add topology parsing of some protein residues, waters, ions, and generic molecules. * Miscellaneous improvements * Update amino acids and nucleotides list * Various fixes to XML writing, and separate XML writing into a new class * Comments/warnings * Add nucleic topological definitions * Improved handling of peptide residues * Fix for CYX (disulfide bonds) * Refactor the topology creation methods * General improvements, and add support for nucleic-like residues * No need to handle MP, DP, TP * Minor improvements * General refactoring, add automatic determination of topology * Add TinkerAtomType dataclass, and remove references to biotypes as they are not needed * Re-add missing parsing of forces and scalars * Updates to createSystem() * Add AMOEBA forces * Add angle-related forces to createSystem * Add placeholders for missing forces * Beginning of support for AmoebaMultipoleForce * Finished support for AmoebaMultipoleForce * Support for AmoebaVdwForce * TinkerFiles supports vdw * Misc updates, and add AmoebaTorsionTorsion, AmoebaWcaDispersion, and AmoebaGeneralizedKirkwood * Remove XML writer * Fixes * Fix wrong indentation in _findBitorsions * Remove pdb debugging * Documentation and fixes * Remove files * Revert checks in AmoebaVdwForceBuilder and ## @private markers * Remove duplicated static methods _getChiralAtomIndex * Fix GK force * Fix WcaDispersion force * Fix WcaDisp * Fixes and updates * Cleanup and removing duplicated code * Bug fixes * A few more unit conversions * Minor cleanup * Misc fixes and updates * Fix Add AmoebaStretchBendForce * Simplify force builders * Update ForceField * Fix AmoebaPiTorsionForce * Only add AmoebaWcaDispersionForce if using implicitSolvent * Simplify amoebaforces * Stretch torsion and angle torsion * Misc. fixes * Improve tests * Fix cap group identification * Add/improve tests * Remove whitespaces from residue names * Improve tests * Consistent use of atomClasses list * Fix match condition in AmoebaOutOfPlaneBendForceBuilder * Fix AmoebaStretchBendForce * Final fix for AmoebaStretchBendForce * Fix AmoebaAngleForce * Small fixes and improvements * Update assertion tolerances * Simplify torsion-torsion force creation * Small fixes in the tests * Review comments, type hints, docs for tinkerfiles.py * Only use standard PDB for AA * Type hint and docs for amoebaforces * Reduce tolerances for failing tests * Fixed error with ZOnly axis type when x particle is not specified --------- Co-authored-by: peastman <peastman@stanford.edu>
15 lines
713 B
Python
15 lines
713 B
Python
from openmm.app import *
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from openmm import *
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from openmm.unit import *
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from sys import stdout
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tinker = TinkerFiles('amoeba_solvated_phenol.xyz', ['amoeba_phenol.prm', 'amoebabio18.prm'])
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system = tinker.createSystem(nonbondedMethod=PME, nonbondedCutoff=0.7*nanometer, vdwCutoff=0.9*nanometer)
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integrator = LangevinMiddleIntegrator(300*kelvin, 1/picosecond, 0.001*picoseconds)
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simulation = Simulation(tinker.topology, system, integrator)
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simulation.context.setPositions(tinker.positions)
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simulation.minimizeEnergy()
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simulation.reporters.append(DCDReporter('output.dcd', 1000))
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simulation.reporters.append(StateDataReporter(stdout, 1000, step=True, potentialEnergy=True, temperature=True))
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simulation.step(10000)
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