[gmx-users] How to get a equilibriumed system effectively

David van der Spoel spoel at xray.bmc.uu.se
Thu Nov 23 18:30:45 CET 2006

Qiao Baofu wrote:
> Hi all,
> Now I meet a problem when building a system.  I used prodrg to get the 
> .pdb of a single molecule, write the .top file manually. The 
> single-molecule system is equilibriumed (em, NVE, NTV,NTP are all ok for 
> at least 1 ns). Then I used  two method  to get a bigger (8 molecules) 
> system: 1) genbox -cs -box; 2) genbox -nmol -ci -cp. Both result are ok 
> when EM. But when NVE is runn, result 2 crashed right now . For results 
> 1, NVE is ok, and short-time NTV and NTP(about 10ps) are ok, but 
> long-time NTV  and NTP(1ns) crashed with the same reason.
> On the other hand, I build a very dilute sytem (5 molecules, density is 
> about 2 g/l). It runs very well. But the problem is it is very hard to 
> converge to the suitable density (1000 g/l).
> Who knows how to solve it? Thanks a lot. 
> Program mdrun, VERSION 3.3.1
> Source code file: nsgrid.c, line: 226
> 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 -2147483648. It should have been within [ 0 .. 1000 ]
> Please report this to the mailing list ( gmx-users at gromacs.org 
> <mailto:gmx-users at gromacs.org>)
> -------------------------------------------------------
> -- 
> ****
> Baofu Qiao
> ------------------------------------------------------------------------
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You can scale the system size by coupling to a pressure of e.g. 1000 
bar, use a cutoff rather than PME to speed up this bit. Then, when your 
system is condensed you re-equilibrate with normal pressure coupling and 

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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