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.
Mark
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