[gmx-users] Energy per residue

[Justin A. Lemkul]

afsaneh maleki wrote:
> 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 .
>  
>  

As I said before, as an absolute, "energy per residue" is not a straightforward 
term, and even if it was, likely has no physical meaning.  The potential energy 
function is complicated, depending upon the positions of all the particles in 
the system; that is, nearby particles will interact via Coulombic and vdW 
interactions, but you can't simply extract out either of these terms for any 
specific residue.  There are numerous useful posts in the list archive on 
similar topics, for example:

http://lists.gromacs.org/pipermail/gmx-users/2007-October/030425.html

-Justin

>  
> 
> Best wishes, 
> Afsaneh
> 
> 
>  
>  
>  
> 
>     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
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 

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

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

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