[gmx-users] pressure scaling more than 1%

[Justin A. Lemkul]

杜波 wrote:
> 
> 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.

Please consult:

http://www.gromacs.org/Documentation/Errors#Pressure_scaling_more_than_1.25
http://www.gromacs.org/Documentation/Terminology/Blowing_Up

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.

-Justin

> thanks!!
> 
> step 112000, will finish Sun Dec 11 03:59:40 2011
> Step 112002  Warning: pressure scaling more than 1%, mu: 48937.5 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
> 
> 
> regards,
> 
> 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>
> 

-- 
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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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