Re: [AMBER] DIELC constant for normal mode analyses in vacuum ?

From: Toshifumi Yui <>
Date: Fri, 24 Jun 2011 16:11:34 +0900

湯井 敏文 Ph.D. (准教授)
〒889-2192 宮崎市学園木花台西1-1
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-----Original Message-----
From: David A. Case
Sent: Friday, June 24, 2011 11:35 AM
To: AMBER Mailing List
Subject: Re: [AMBER] DIELC constant for normal mode analyses in vacuum ?

On Thu, Jun 23, 2011, Marek Maly wrote:
> So could you say some recommendation about the DIELC parm. from @NM
> section regarding normal mode analyses in vacuum ?

For the purposes of getting a rough estimate of harmonic entropies, using
default values is probably's been used a lot. But I personally
use the python version, which uses GB theory to get normal modes. These
to provide strutures that are (to a small but non-negligable extent) closer
solution structures than those that use a 4r dielctric constant.

Note that the point of using either GB or epsilon=4r is *not* to simulate
system in vacuum, but to have an implicit solvent model, that is, one that
no explicit solvent molecules, but which nevertheless mimics the behavior of
the solute in solution. So, it just "looks like" a vacuum simulation, but
goal is to get an estimate of solvated properties. [So I really
misunderstood your goal in my previous reply.]

...hope this helps...dac

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