[gmx-developers] Force calculation

Chenyue Xing cxing at ucdavis.edu
Tue Oct 17 01:33:43 CEST 2006

Dear developers,

For non-bonded interactions, I know there's force-calculation carried out in
nb_kernel. Is there any other place in the code involving a calculation of
interactions? For example, the neighborlist setting part?

I noticed that in the nb_kernel code, it first computes the distances
between 2 atoms, then uses that distance r to look-up for energy and force
values from VFtab[] array. Then it computes the force components fx, fy, fz.

I want to test a new interaction type with z-dependence only. So I first set
r =z instead of r=sqrt(x^2+y^2+z^2),but this won't work. But if I keep r as
the original, then eliminate the fx, fy components to have a force in z
direction only, the program works fine.
As what I really expect is the first r=z case, I wondered if it's b/c of the
system not equilibrated (I saw a sudden increase in distance which led to a
huge nnn so that VFtab[nnn] out of bound). So I tried to change the nslist
update freq to 1 and the program stuck somewhere, doing nothing. If I use a
nslist update freq >= 2, it'll give a huge distance after say 4 steps and
segmentation faulted.

I wonder if gromacs computes the force when setting up the neighborlist for
efficiency. If anyone can help me with the force calculation info, it'll be
of great help for me to track down the error.
Sorry for the long and messy email and looking forward to the replies!!

Any response is highly appreciated!!
Thank you very much for your time.

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