Troubleshooting NaN Errors in OpenMM

[Andrew Orry]

Q: I received an error saying “Particle coordinate is NaN” when running MD in ICM. What does this mean?
A: This indicates a numerical error occurred during the simulation - the particle coordinates became undefined (NaN = Not a Number).

You can refer to the OpenMM FAQ here:
https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#nan

You can often fix it by slightly randomizing the receptor atom positions and then re-running the simulation.

Use the following command - replace MyObject with the name of your object

randomize 0.001 a_MyObject.//