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Date:
2018-11-30 21:55 		Priority:
3
State:
Open
Submitted by:
Nobody 		Assigned to:
Nobody (None)
Resolution:
none
Summary:
Particle

Detailed description
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?

Add A Comment: Notepad

Message  ↓
Date: 2018-12-03 20:45
Sender: Peter Eastman

Monitoring the forces during your simulation, I see the problem is being caused by a huge force between particles 276 and 291. It seems that something is steadily pushing them apart, until the force of the harmonic bond connecting them becomes too large and the simulation blows up. I'm not sure what it is about your system that causes this to happen. You seem to have different forces that are fighting with each other, leading to instability.

Attachments:
Size Name Date By Download
1 KiBOpenMM_equilibrate.py2018-11-30 21:55NoneOpenMM_equilibrate.py
932 KiBAcacetin_m.prmtop2018-11-30 21:55NoneAcacetin_m.prmtop
198 KiBAcacetin_m.inpcrd2018-11-30 21:55NoneAcacetin_m.inpcrd
Field Old Value Date By
detailsAnonymous 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?2018-12-03 20:45peastman
File Added660: OpenMM_equilibrate.py2018-11-30 21:55None
File Added661: Acacetin_m.prmtop2018-11-30 21:55None
File Added662: Acacetin_m.inpcrd2018-11-30 21:55None

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