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

[David van der Spoel]

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 
PME.

-- 
David.
________________________________________________________________________
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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