VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Nov 28 2016 - 00:15:51 CST

Hi,
  If you are doing very simple pairwise calculations, there are
"measure energy" commands in VMD to measure pairwise energies
if you have the necessary force field parameters for the
pairs of atoms you want to measure values for. For more the perhaps
more common and inherently more complex scenarios, you would likely
best calculate these quantities within NAMD, Gromacs, or whatever your
favorite MD engine is, rather than in VMD. This is particular true
if you're comparing the values vs. other quantities that might be measured
in an MD simulation.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Nov 22, 2016 at 05:22:49PM +0530, Seera Suryanarayana wrote:
> Dear VMD users,
>
> I would like to find the vander waal interactions of PDB of my
> interest. Kindly tell me how to do it.
>
> Thanks in advance
> Surya
> Graduate student
> India. 

-- 
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/