[gmx-users] NaN error for mdrun-gpu

Adam Jion adamjion at yahoo.com
Wed Feb 29 03:34:56 CET 2012


I have a Palit 3GB GTX 580 GPU card to simulate about ~ 140 000 atoms.
However, after an mdrun-gpu simulation of 5000 timesteps (each time step = 0.002), the log file starts to show NaN in the energy values.

How do I fix this?


ps. The same system runs well in a conventional CPU-based mdrun. So I don't think its due to the system blowing up.
pps. The GPU card reaches a temperature of ~ 88 degrees celsius after 5 minutes of simulation. Could this be the problem? However, I have another GPU card (MSI 1.5GB GTX 580) that works well with a smaller system (100 000 atoms) even at 85 degrees celsius.
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