[gmx-users] Energy per residue

afsaneh maleki maleki.afsaneh at gmail.com
Fri Mar 12 23:03:30 CET 2010

Dear Justin,

I want to get energy per residue not time. if i use mdrun -rerun  with
energygrps in md.mdp  then g_energy i obtain enery per time not residue.
at last, i don't understand how to get Energy per residue .

Best wishes,

> afsaneh maleki wrote:
>> Dear gromacs users,
>>  Is there a way to get energy values (Vdw,..) per residue at the end of MD
>> prosses?
> Yes and no.  You won't be able to get, for instance, the absolute van der
> Waals energy of a residue.  That doesn't really make any sense, since vdW
> interactions take place between particles.  There may be some 1-4 type
> interactions within a residue that you could quantify, but not much else.
> You can decompose short-range residue-residue energies using energygrps in
> the .mdp file, and re-running the trajectory with the new .tpr file (mdrun
> -rerun), but the .edr file can quickly get out of hand in terms of disk
> usage, depending on how many groups you have (since you will then have
> essentially N^2 energy terms to write out, where N is the number of
> energygrps).
> -Justin
>  I would really appreciate any help.
>> Afsaneh
> --
> ========================================
> 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
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