[gmx-users] Pairwise forces
Mark.Abraham at anu.edu.au
Fri Nov 19 17:54:05 CET 2010
On 19/11/2010 10:15 PM, Reiner Ribarics wrote:
> Dear all,
> I know similar topics have already been discussed, but there is a
> question regarding pairwise forces that could not be resolved by
> reading the mailing list.
> Our group has already done some rather long simulations and according
> to the script files forces are written every 10000 steps and can be
> accessed via trjconv with -cf option that assigns each atom a
> temperature factor. I was wondering if that is the way gromacs stores
> the forces in the trajectory file. Or are the temperature factors
> calculated from other (maybe pairwise) forces?
A trajectory file of T frames of N atoms containing only forces is
simply T sets of 3*N numbers interleaved with some per-frame header
information. There is no way to decompose anything "after the fact".
g_traj works from those forces.
> I also had a look at FDA gromacs that is able to write out pairwise
> forces, but unfortunately it falls back on the rather slow gromacs
> routines and we want to avoid rerunning our simulations if possible.
Anything that computes pairwise forces will necessarily be slow, or a
memory-hog, or both.
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users