Nimesh Jain wrote:
Hi,
I keep getting the following error when I do mdrun:
During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
I moved the particles sufficiently apart so that there are no overlaps.
I still get this error. Can someone tell me what else can I do?
Please let me know if you need any other info.
An .mdp file, a description of your system, and a list of commands that shows
how you built it would be required to get any useful advice. Otherwise, the
standard advice is (as always) found here:
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
Troubleshooting tips are listed there.
-Justin
Thanks,
Nimesh
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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