VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Apr 28 2015 - 16:34:47 CDT

On Tue, Apr 28, 2015 at 6:03 AM, Subrata Paul <paul.subrata34_at_gmail.com> wrote:
> Actually I have simulated a protein-urea-water system and want to know pair
> wise electrostatic and vdw interaction energy. In the vmd energy tool the
> default dielectric constant is 1.
>
> 1. Is it correct for explicit solvent ? what will be the dielectric constant
> in protein-urea and protein-water interaction?

you will need to use whatever you have used in your simulation. if you
have not explicitly set it, it will have been 1. in general, you have
to match all relevant settings with those of your simulation(s) or
else the results from namdenergy will be useless.

> 2. is dielectric constant required for only electrostatic energy ?

yes.

>
> --
> With Best Regards
> Subrata Paul
> PhD Student
> Dept of Chemistry.
> IIT Guwahati
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.