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@gromacs.org
<mailto:gmx-users@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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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