Re: NAMD electrostatic interaction Failure.

From: Kenno Vanommeslaeghe (
Date: Thu Sep 26 2013 - 16:59:20 CDT

Dear Mehran,

The answers you need are already in my previous e-mail; you seem to lack
the necessary background to understand them. Unfortunately, I don't
currently offer a "molecular modelling 101" correspondence course, and
neither is that the function of this mailinglist.

On 09/26/2013 11:12 AM, Mehran MB wrote:
> by considering 1 for dielectric constant for all atoms in the presence of
> molecule of water (explicit model), should one get the same results as
> considering 80 for dielectric constant and lack of molecule of water
> (implicit Model) !?!

Most certainly not. The dielectric approximation breaks down (pun
intended) at the microscopic level; things become much more complex.
Accordingly, current implicit solvent models are more complex than a
simple adjustment to the dielectric constant (yet still very much
different from explicit solvent).

There are a number of standard procedures to obtain the information you're
looking for. These methods have been well thought-out by smart people,
have withstood the scrutiny of the scientific community, and their
strengths and weaknesses have been characterized through years of usage.
What you should do is:
- discuss with your mentor which one of these methods would be most
optimal for your purpose (probably something like MM/PBSA or MM/GBSA),
- look up information on how to use the chosen method,
- try it for yourself and try to troubleshoot any problems that surface,
- come back and ask questions if you get stuck.

I am not you mentor or co-author and I don't have time to help you through
the process step-by-step; that's not the function of this mailinglist either.

Best regards,


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