Detailed description |
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Anonymous message posted by jy634@cornell.edu
Hi all,
I've been trying to simulate the following example and have been getting the Particle coordinate is nan exception, producing following result:
Traceback (most recent call last):
File "OpenMM_equilibrate.py", line 30, in <module>
simulation.step(500000)
File "/home/jeewon/anaconda3/lib/python3.6/site-packages/simtk/openmm/app/simulation.py", line 132, in step
self._simulate(endStep=self.currentStep+steps)
File "/home/jeewon/anaconda3/lib/python3.6/site-packages/simtk/openmm/app/simulation.py", line 194, in _simulate
self.integrator.step(10) # Only take 10 steps at a time, to give Python more chances to respond to a control-c.
File "/home/jeewon/anaconda3/lib/python3.6/site-packages/simtk/openmm/openmm.py", line 17086, in step
return _openmm.LangevinIntegrator_step(self, steps)
Exception: Particle coordinate is nan
The installation looks fine to me:
There are 4 Platforms available:
1 Reference - Successfully computed forces
2 CPU - Successfully computed forces
3 CUDA - Successfully computed forces
4 OpenCL - Successfully computed forces
Median difference in forces between platforms:
Reference vs. CPU: 1.97982e-05
Reference vs. CUDA: 2.15102e-05
CPU vs. CUDA: 1.55367e-05
Reference vs. OpenCL: 2.15121e-05
CPU vs. OpenCL: 1.55499e-05
CUDA vs. OpenCL: 1.1684e-07
and I'm using OpenMM 7.1.
"energy = simulation.context.getState(getEnergy=True).getPotentialEnergy()" line gives me back the following:
-26889.394957613025 kJ/mol
Can someone help me identify the issue? |
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