Created
December 1, 2021 22:49
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| from MDAnalysis.coordinates.DCD import DCDFile | |
| dms = app.DesmondDMSFile('a.dms') | |
| system = dms.createSystem(nonbondedMethod=app.PME, | |
| nonbondedCutoff=9.0*unit.angstroms,OPLS=True) | |
| import simtk.openmm as openmm | |
| system.addForce(openmm.MonteCarloBarostat(1 * units.bar, 300*unit.kelvin)) | |
| integrator = mm.LangevinIntegrator(300*unit.kelvin, 1.0/unit.picoseconds, | |
| 2.0*unit.femtoseconds) | |
| integrator.setConstraintTolerance(0.00001) | |
| platform = mm.Platform.getPlatformByName('CUDA') | |
| properties = {'CudaPrecision': 'single'} | |
| simulation = app.Simulation(dms.topology, system, integrator, platform, | |
| properties) | |
| import mdtraj as md | |
| a=md.load('a.dcd', top='a.pdb') | |
| index1=0 | |
| with DCDFile("a.dcd") as dcd: | |
| header = dcd.header | |
| for frame in dcd.readframes()[0]: | |
| simulation.context.setPositions(frame * unit.angstrom) | |
| simulation.context.setPeriodicBoxVectors(a=a.unitcell_vectors[index1][0],b=a.unitcell_vectors[index1][1],c=a.unitcell_vectors[index1][2]) | |
| state = simulation.context.getState(getForces=True,getEnergy=True) | |
| print(state.getPeriodicBoxVectors()) | |
| print(state.getPotentialEnergy()/unit.kilocalories_per_mole) | |
| index1=index1+1 |
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