Particle Coordinate is NaN occasionally upon molecule hitting PBCs about openmm

[alexberlaga]

After trying many things, increasing the friction coefficient to 1/ps seems to make this PBC issue go away. I am not yet fully convinced that it's not a coincidence, but the more simulations I run with this friction coefficient, the more I'm confident that it's the case.

[peastman]

Hopefully that's all it takes. For what it's worth, 1/ps is the default value I usually recommend. Your previous value of 0.01/ps is tiny. It takes hundreds of picoseconds to exchange energy between the system and the heat bath. That doesn't make it less accurate, but it does mean any inaccuracy in the simulation (like from the finite time step) has a lot more opportunity to cause problems.

[alexberlaga]

Could such an error occur because of a very low constraint tolerance (maybe the integrator is doing something crazy to enforce a desired temperature)? I noticed that mine is 1e-8, while others in these posts have used tolerances of 1e-5 or 1e-6.

[peastman]

Your code uses mixed precision, right? If so, it shouldn't be a problem. 1e-8 is smaller than it's possible to achieve in single precision, which in that case could lead to problems. But in mixed precision the only issue would be slower performance since it needs more iterations to converge the constraints.

[alexberlaga]

It seems like this could be a CVPack issue, rather than an openmm issue... when I added a new "force" through CVPack that simply keeps track of certain distances [ cvpack.Distance( ... , pbc=True) ], these errors started popping up again decently often.