[gmx-users] Taking difference of forces in two trajectories
Justin A. Lemkul
jalemkul at vt.edu
Fri Apr 1 00:19:43 CEST 2011
Sikandar Mashayak wrote:
> hey thanks for the explanation..
> for some constraints I need to have the difference of forces in the
> .trr format so that I have position,velocity and force error values in
> one single .trr file. , I dont think g_traj would help me getting that..
> is there any other option?
I don't think there is currently any tool that can do this. With the xdrfile
library, though, you might be able to write your own program that can do it.
> On Thu, Mar 31, 2011 at 4:44 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
> Sikandar Mashayak wrote:
> 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 A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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