[gmx-users] Formula for cosine content in essential dynamics

Yin Jian smayinj at nus.edu.sg
Tue Aug 28 07:50:37 CEST 2007

Hi All,
Can anybody tell me more than that in the gromacs manual, how Gromacs
calculate g_sas. What are their criteria basis on hydrophobic and

Thanks in adv.


-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Berk Hess
Sent: Monday, August 27, 2007 10:56 PM
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] Formula for cosine content in essential

>From: "Steve Spronk" <spronk at umich.edu>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: "'Discussion list for GROMACS users'" <gmx-users at gromacs.org>
>Subject: RE: [gmx-users] Formula for cosine content in essential
>Date: Mon, 27 Aug 2007 09:18:30 -0400
>Thank you, Berk, for clearing it up for me.  I thought that maybe I
>understand something fundamental to the method.  The formula lacking
>is in quite a few papers as well as the Gromacs manual.  It has escaped
>attention so far probably because g_analyze takes care of the

It's probably the same piece of latex formula that I just cut and pasted

several times.
Shame on me for not checking better...


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