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

Qiao Baofu qiaobf at gmail.com
Thu Nov 23 17:21:37 CET 2006

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)

Baofu Qiao
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