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

[Justin A. Lemkul]

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.

-Justin

> 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:
> 
>         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 <http://vt.edu> | (540) 231-9080
>     <tel:%28540%29%20231-9080>
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
>     -- 
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at
>     http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>     Please don't post (un)subscribe requests to the list. Use the www
>     interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> 

-- 
========================================

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

========================================