verbose pdb analysis and energy minimization
Posted: Mon Dec 21, 2015 5:01 pm
Hi everyone,
does anyone know how to get extra insight from
A.
energy minimization
B.
reading pdb
I'm using a protonated and optimized protein with a script created based on Robert's app http://builder.openmm.org/
the problem is that everything explodes shortly after I start relaxation run following the energy minimization with a very tight threshold.
The output of MD relaxation looks like something (probably hydrogens) are not connected in the topology file and probably are causing nonbonded clashed but pdb.getTopology() gives a very llimited output
the problem is that everything explodes shortly after I start relaxation run following the energy minimization with a very tight threshold.
The output of MD relaxation looks like something (probably hydrogens) are not connected in the topology file and probably are causing nonbonded clashed but pdb.getTopology() gives a very llimited output
does anyone know how to get extra insight from
A.
energy minimization
B.
reading pdb
I'm using a protonated and optimized protein with a script created based on Robert's app http://builder.openmm.org/
the problem is that everything explodes shortly after I start relaxation run following the energy minimization with a very tight threshold.
The output of MD relaxation looks like something (probably hydrogens) are not connected in the topology file and probably are causing nonbonded clashed but pdb.getTopology() gives a very llimited output
Code: Select all
from __future__ import print_function
from simtk.openmm import app
import simtk.openmm as mm
from simtk import unit
from sys import stdout
from simtk.unit import *
pdb = app.PDBFile('MOE_FIX.pdb')
forcefield = app.ForceField('amber10.xml', 'amber10_obc.xml')
system = forcefield.createSystem(pdb.topology,
nonbondedMethod=app.CutoffNonPeriodic, nonbondedCutoff=2.0*nanometers)
integrator = mm.LangevinIntegrator(300*kelvin, 1.0/picoseconds,
0.5*femtoseconds)
#integrator.setConstraintTolerance(0.00001)
platform = mm.Platform.getPlatformByName('CUDA')
properties = {'CudaPrecision': 'mixed', 'CudaDeviceIndex': '0'}
simulation = app.Simulation(pdb.topology, system, integrator, platform,
properties)
simulation.context.setPositions(pdb.positions)
print('Minimizing...')
simulation.minimizeEnergy(tolerance=0.1*kilojoule/mole)
#simulation.reporters.append(app.DCDReporter('equilibrate.dcd', 1000))
#simulation.reporters.append(app.PDBReporter('equilibrate.pdb', 1000))
simulation.reporters.append(app.StateDataReporter(stdout, 1, step=True,
potentialEnergy=True, temperature=True,
totalSteps=10000,separator ='\t' ))
simulation.context.setVelocitiesToTemperature(10*kelvin)
print('Equilibrating...')
simulation.step(10000)
#simulation.reporters.append(app.DCDReporter('trajectory.dcd', 10000))
#simulation.reporters.append(app.PDBReporter('trajectory.pdb', 10000))
#simulation.reporters.append(app.StateDataReporter(stdout, 10000, step=True,
# potentialEnergy=True, temperature=True, progress=True, remainingTime=True,
# speed=True, totalSteps=100000, separator='\t'))
#print('Running Production...')
#simulation.step(10000)
print('Done!')
The output of MD relaxation looks like something (probably hydrogens) are not connected in the topology file and probably are causing nonbonded clashed but pdb.getTopology() gives a very llimited output
Code: Select all
Minimizing...
Equilibrating...
#"Step" "Potential Energy (kJ/mole)" "Temperature (K)"
1 4.72611915361e+11 12326086179.3