[gmx-users] force evaluation

Mark Abraham Mark.Abraham at anu.edu.au
Mon Jan 5 22:45:05 CET 2009

Silvia Crivelli wrote:
> Hello,
> 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 
> this
> 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 


More information about the gromacs.org_gmx-users mailing list