[gmx-users] Pairwise forces

[Bogdan Costescu]

On Fri, Nov 19, 2010 at 12:15, Reiner Ribarics
<reiner.ribarics at meduniwien.ac.at> wrote:
> 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?

It's not clear to me what you try to do. Obtain atomic forces ? Obtain
pairwise forces ? Know the format in which forces are stored in the
trajectory file ? Something else entirely ?

> 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.

Then please take a look again. The forces are indeed saved by hooking
into the C kernels, but in a 'mdrun -rerun' phase which reads back the
trajectory and writes the forces, which avoids having a compute
intensive phase with the C kernels and the FDA modifications.

Kind regards,
Bogdan