Re: NAMD electrostatic interaction Failure.

Date: Thu Sep 26 2013 - 17:27:31 CDT

Dear Kenno,

I just repeat my question to make it clear that I am looking for some way
to calculate electrostatic interaction and see if NAMD calculation is
reasonable. I was looking for a clue and I am going to take your advice and
respect your time.

thank you for your consideration.

All the best,


On Thu, Sep 26, 2013 at 5:59 PM, Kenno Vanommeslaeghe <> wrote:

> 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,
> Kenno.

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