[gmx-users] REMD: NPT being +-Infinity or NaN

Justin A. Lemkul jalemkul at vt.edu
Mon Nov 28 04:36:08 CET 2011

杜波 wrote:
> dear teacher,
> when i do remd  in the  npt ensemble.
> REMD: NPT -replex 4000
> dt= 0.0001
> step 172000, will finish Sat Dec 31 18:44:12 2011
> -------------------------------------------------------
> Program mdrun_mpi_4.5.5, VERSION 4.5.5
> Source code file: nsgrid.c, line: 549
> Range checking error:
> Explanation: 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.
> how could  i do except using the small dt ? 

Your system is not stable, as is often the case with NPT REMD at high temperature.




Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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