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湯井 敏文 Ph.D. （准教授）
宮崎大学工学部物質環境化学科
〒889-2192 宮崎市学園木花台西1-1
電話 0985－58－7319
ファックス 0985－58－7323
E-mail tyui.cc.miyazaki-u.ac.jp
URL
http://www.chem.miyazaki-u.ac.jp/~webms/index.htm
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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
the
default values is probably OK...it'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 Fri Jun 24 2011 - 00:30:05 PDT
