[gmx-users] ns_type=grid leads to blowups in minimization but not with ns_type=simple
David van der Spoel
spoel at xray.bmc.uu.se
Wed Mar 22 20:08:13 CET 2006
David Mobley wrote:
> Dear all,
> I've been having some very sporadic problems with minimization (that
> is, only on some of the many systems I minimize). In some cases,
> during steepest descent minimization (following L-BFGS, which
> essentially ends immediately for the system in question), minimization
> runs for about 10 steps, and then I get an error about a water
> molecule that couldn't be settled, followed by the following:
> 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 .. 1521 ]
> Please report this to the mailing list (gmx-users at gromacs.org)
> Strangely enough, if I switch ns_type from grid to simple, everything
> seems to work fine.
> Does anyone have any idea why this might be? Is there some reason
> ns_type=grid shouldn't work right for minimization? Or is there a bug?
> (I can submit a bugzilla with input files and so on, but first I
> wanted to make sure I'm not doing something stupid).
If there's no bugzilla there isn't a bug. Please upload two tpr files
with the only difference being the NS type that sow the mentioned behavior.
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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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