[gmx-developers] VFtab index too large

[Chenyue Xing]

My neighborlist is set to be updated every 10 steps. It core dumped in the
4th loop (outloop index n=4). From the printed-outs, in the first 3 loops,
the neighborlists seem to be stable.

On 9/23/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> Chenyue Xing wrote:
> > Hi David, Erik and other developers,
> >
> > You might remember I posted several questions related to the C codes
> > (nb_kernelxyz) weeks ago.
> > I've been trying to make a z-dependent only LJ interaction.
> > Once I make rsq=dz*dz (instead of rsq=dx*dx+dy*dy+dz*dz), after a
> > certain number of loops and steps, the coordinates of one neighbor
> > atom get quite large (of the order of 10^5), making rsq even larger.
> > As r is then used to computer the index of VFtab, nnn, this leads to a
> > nnn of the order of 10^9 and of course, the program cannot reach the
> > memory address of VFtab[1000000000]. So it goes to a segmentation fault.
> >
> > I really don't understand why a small change in rsq (my system is a
> > 128 DPPC with water, total 4700 coarse-grained atoms, dx dy is usually
> > around 1 nm for each step as printed out) will result in a sudden bump
> > of pos[] (or rvec x[]) values. If you could shine some light on this
> > issue, it will be very helpful.
> >
> > I appreciate your responses!
> >
> > Chenyue Xing
> How about your neighborlist? Is that updated as it should?
>
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > gmx-developers mailing list
> > gmx-developers at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-developers
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-developers-request at gromacs.org.
>
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-developers-request at gromacs.org.
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20060923/09502692/attachment.html>