[gmx-users] minimization error in gromacs3.3
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?
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.
More information about the gromacs.org_gmx-users