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

[Sikandar Mashayak]

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
> 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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