[gmx-users] pressure scaling more than 1%
Justin A. Lemkul
jalemkul at vt.edu
Sat Nov 5 16:00:14 CET 2011
> Dear teacher,
> when i do remd in the npt ensemble.
> it will be bomb when it run a little time .
> and the dt is 0.00144,(in my opinion ,it is small enough , in this
> condition , the simlution time is about one month )
> how could i do except using a small dt.
Without seeing your .mdp file, there's little more to be said. Please also
search the list archive; such issues have been asked and solved hundreds of
times over and there is certainly some useful information already available.
Also note that high-temperature replicates in REMD may be unstable in an NPT
ensemble, largely because the algorithms break down.
> step 112000, will finish Sun Dec 11 03:59:40 2011
> Step 112002 Warning: pressure scaling more than 1%, mu: 48937.5 48937.5
> 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.
> Variable ci has value 1792617862. It should have been within [ 0 ..
> 330578952 ]
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> Bo Du
> Department of Polymer Science and Engineering,
> School of Chemical Engineering and technology,
> Tianjin University, Weijin Road 92, Nankai District 300072,
> Tianjin City P. R. China
> Tel/Fax: +86-22-27404303
> E-mail: 2008dubo at gmail.com <mailto:2008dubo at gmail.com>
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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