Created
May 18, 2015 20:09
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from __future__ import print_function | |
from simtk.openmm import app | |
import simtk.openmm as mm | |
from simtk import unit | |
from sys import stdout | |
pdb = app.PDBFile('water256_bulk_tip5p.pdb') | |
#pdb = app.PDBFile('a.pdb') | |
#pdb = app.PDBFile('water14_cluster.pdb') | |
boxDim = 19.3996888399961804/10. | |
temperature = 300 | |
boxSize = (boxDim, boxDim, boxDim) * unit.nanometer | |
pdb.topology.setUnitCellDimensions(boxSize) | |
forcefield = app.ForceField('amber10.xml', 'tip5p.xml') | |
################################## NVT | |
system = forcefield.createSystem(pdb.topology, nonbondedMethod=app.PME, | |
nonbondedCutoff=0.9*unit.nanometers, constraints=None, rigidWater=True, | |
ewaldErrorTolerance=0.0005) | |
integrator = mm.VerletIntegrator(0.2*unit.femtoseconds) | |
system.addForce(mm.AndersenThermostat(temperature, 1./unit.picoseconds)) | |
# platform = mm.Platform.getPlatformByName('Reference') | |
platform = mm.Platform.getPlatformByName('CUDA') | |
properties = {'CudaPrecision': 'double'} | |
simulation = app.Simulation(pdb.topology, system, integrator, platform) | |
simulation.context.setPositions(pdb.positions) | |
simulation.context.computeVirtualSites() | |
simulation.context.setVelocitiesToTemperature(300*unit.kelvin) | |
print('Equilibrating...') | |
simulation.step(100) | |
simulation.reporters.append(app.StateDataReporter("tip5p_nvt.log", 50, step=True, time=True, | |
potentialEnergy=True, kineticEnergy=True, totalEnergy=True, temperature=True, | |
progress=True, remainingTime=True, speed=True, totalSteps=500000, | |
separator='\t')) | |
print('Running Production...') | |
simulation.step(500000) | |
print('Done!') | |
final_nvt_state = simulation.context.getState(getVelocities=True, getPositions=True) | |
positions = final_nvt_state.getPositions() | |
velocities = final_nvt_state.getVelocities() | |
################################## NVE | |
system = forcefield.createSystem(pdb.topology, nonbondedMethod=app.PME, | |
nonbondedCutoff=0.9*unit.nanometers, constraints=None, rigidWater=True, | |
ewaldErrorTolerance=0.0005) | |
integrator = mm.VerletIntegrator(0.2*unit.femtoseconds) | |
simulation = app.Simulation(pdb.topology, system, integrator, platform) | |
simulation.context.setPositions(positions) | |
simulation.context.computeVirtualSites() | |
simulation.context.setVelocities(velocities) | |
simulation.reporters.append(app.StateDataReporter("tip5p_nve.log", 50, step=True, time=True, | |
potentialEnergy=True, kineticEnergy=True, totalEnergy=True, temperature=True, | |
progress=True, remainingTime=True, speed=True, totalSteps=500000, | |
separator='\t')) | |
print('Running Production...') | |
simulation.step(500000) | |
print('Done!') |
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