[gmx-users] Taking difference of forces in two trajectories

Justin A. Lemkul jalemkul at vt.edu
Thu Mar 31 23:44:30 CEST 2011

Sikandar Mashayak wrote:
> Hi
> I want to test two test potentials compared to reference potential. 
> I have md trajectories from reference potential. So I do mdrun -rerun 
> with two different test potentials and get two separate trajectory 
> files. Now I want to compute difference between forces acting on each 
> atom in each frame due to different test potentials. Is there any way 
> where two trajectories with same position values but different forces 
> can be used to get third .trr file with forces which are difference of 
> first two?

I don't think you can make mdrun calculate differences in two existing 
trajectories, but you can extract forces using g_traj and take the difference 
between the two output files.  The file sizes may get extremely large for either 
long trajectories or many atoms.


> thanks
> sikandar


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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