VMD-L Mailing List

From: Faezeh Pousaneh (fpoosaneh_at_gmail.com)
Date: Tue Jul 05 2016 - 13:40:07 CDT

thank you John for the information.
Yes, I was helped doing it in Gromacs.

Best regards

On Tue, Jul 5, 2016 at 7:46 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> 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/
>