[gmx-developers] Re: Force calculation

Chenyue Xing cxing at ucdavis.edu
Tue Oct 17 22:49:17 CEST 2006

Hi David,

I actually tried with a 3-atom system first and that worked perfect. Then I
tried a larger system which now has the segfault problem. My conformation is
good at least for normal interactions and the fz only case. Maybe there's
some conflict or inconsistency when I do a r=z case?
As the huge r first appeared in the 4th step (I suspected there's
inequilibrium in the system), I used a more frequent nblist update to see if
it can avoid that but no luck. And a nblist_update freq=1 gives stuck
(infinite loop somewhere maybe?). So would you come across any guess that I
might unfortunately do anything bad with the neighborlist codes (I haven't
modified the neighborlist codes though).

Thank you very much!

On 10/17/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> Chenyue Xing wrote:
> > Hi David,
> >
> > I want to use just a LJ potential for a z-dependent only interaction. I
> > noticed that 1/r^n and 1/r^(n+1) are used for energy and force
> > calculation so I tried to set r = z only.
> >
> > Hope you can give me more advices.
> > Thank you very much!
> >
> >
> I don't see why it shouldn't work, except when your starting
> conformation is bad (or a programming error of course). Try with a two
> particle test system first.
> --
> 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
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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