VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 05 2016 - 12:46:48 CDT

Hi,
  If your simulation was done with Gromacs, then you may want to to check if
there are any Gromacs tools for this analysis since you'll likely want your
energy values to be self-consistent with other energies from the MD simulation,
which would mean you should use the same force field. There is a NAMD energy
evaluation plugin you could use, but that would involve using the CHARMM
force field, which would be inconsistent with your Gromacs run.

Cheers,
  John

On Fri, Jul 01, 2016 at 09:41:40AM +0200, Faezeh Pousaneh wrote:
> Hi
> Does someone know how to obtain energy between specific molecules in the
> system (atom slection)? My simulation has been done in Gromacs. any
> plugin?
> thanks,
> Best regards 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/