[gmx-users] Pairwise forces

[Mark Abraham]

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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