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

[Justin A. Lemkul]

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.

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin

-- 
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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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