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

From: David A. Case <>
Date: Thu, 23 Jun 2011 22:35:40 -0400

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 the
default values is probably's been used a lot. But I personally would
use the python version, which uses GB theory to get normal modes. These seem
to provide strutures that are (to a small but non-negligable extent) closer to
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 the
system in vacuum, but to have an implicit solvent model, that is, one that has
no explicit solvent molecules, but which nevertheless mimics the behavior of
the solute in solution. So, it just "looks like" a vacuum simulation, but the
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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Received on Thu Jun 23 2011 - 20:00:03 PDT
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