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.
-Justin
thanks
sikandar
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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