[gmx-users] potential energy

[Justin A. Lemkul]

rams rams wrote:
> Hi,
> I run a regular MD on a peptide with several conformations. I want to 
> estimate the potential energy of each conformer. When I try using 
> "g_energy" with the option of "Potential" using the corresponding ".edr" 
> file, I am getting the average potential energy. But I am thinking that 
> it is the average potential energy of the system rather than the peptide 
> alone (correct me if I am wrong). There is no option with "g_energy" to 
> use an index file. Also I am not sure is there any way I can create the 
> ".edr" file for the peptide alone ? 

The other output of g_energy is energy.xvg, which corresponds to the energies 
over the course of the simulation.  You might be able to map different frames to 
the corresponding energy...

I would think that trying to extract a "potential energy" of just a peptide 
would be meaningless, because its behavior is also dependent upon the 
surrounding environment (e.g., solvent) so to do so would make no sense anyway.

-Justin

> Also let me know in case any other command would do the trick ?
> Thanks in advance.
> Ram.
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> 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/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/mailing_lists/users.php

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

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

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