[gmx-users] force evaluation
Mark.Abraham at anu.edu.au
Mon Jan 5 22:45:05 CET 2009
Silvia Crivelli wrote:
> I need to calculate the forces (derivatives) for every atom in a protein
> as this is being locally minimized using mdrun.
> When I run mdrun I can get the maximum force F-max and the atom on which
> force is evaluated printed in the log file (for example,
> "F-max = 2.20323e+03 on atom 2641 ".)
> I need to be able to compute the force value on every atom of the protein.
> How can I do this with Gromacs?
> I set the parameter nstfout = 10 in my .mdp file but this doesn't seem
> to make a difference.
"nstfout = 10" writes the per-atom forces to the trajectory file every
10 steps, which you can verify with gmxcheck and/or gmxdump. I haven't
verified that these actually get written for energy minimization, and
they probably wouldn't get written at all if your EM doesn't get to 10
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