[gmx-users] Pairwise forces
reiner.ribarics at meduniwien.ac.at
Mon Nov 22 08:36:17 CET 2010
Thanks a lot for the replies.
What we would like to have are the pairwise forces. I, however, was not
sure if gromacs saves the pairwise forces to the trajectory file or not
(I now figured out with gmxdump that atomic forces are saved).
I also came across the mdrun -rerun option, but I was not entirely sure
if it would save me time. I will give it a try with FDA gromacs.
Am 20.11.2010 15:47, schrieb 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)
> 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,
Mag. Reiner Ribarics
Unit for Medical Statistics and Informatics
Section for Biomedical Computersimulation and Bioinformatics
Medical University of Vienna
Spitalgasse 23, BT88
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