[gmx-users] minimization error in gromacs3.3

jjvc jair at iq.ufrj.br
Fri Dec 16 19:16:13 CET 2005

On Friday 16 December 2005 14:53, David van der Spoel wrote:
> jjvc wrote:
> >I did an upgrade of gromacs (3.2.1 --> 3.3)
> >I run a test in my system in which I performe an energy minimization.
> >I used the same files but an error occur:
> more details please. is this the same tpr or a new one? compare them
> with gmxcheck.
> >______________________________________________________________________
> >Program mdrun_d, VERSION 3.3
> >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 .. 1120
> > ] Please report this to the mailing list (gmx-users at gromacs.org)
> >______________________________________________________________________
> >
> >Can you help me?
> >
> >jjvc

In the very beginning there's no tpr yet. I took the last frame of a 10ns 
dynamics performed with mdrun (3.2.1). I'mḿ trying to minimize to do a normal 
mode analysis with this version of gromacs.

I run the following:

grompp_d -n  -f lbfgs1.mdp -c prot.gro   -o lbfgs1.tpr   -p prot.top
mdrun_d   -v -s lbfgs1.tpr    -o lbfgs1.trr -c lbfgs1.g96 -g m1.log -e  

where prot.gro is the last frame cited above

I did this for the previous version of gromacs and no errors were reported.


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