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

Sikandar Mashayak symashayak at gmail.com
Thu Mar 31 23:52:58 CEST 2011

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?

On Thu, Mar 31, 2011 at 4:44 PM, Justin A. Lemkul <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
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
> --
> gmx-users mailing list    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.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110331/bab6ea0f/attachment.html>

More information about the gromacs.org_gmx-users mailing list