[gmx-users] g_sas

[David van der Spoel]

Yin Jian wrote:
> 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
> hydrophilic? 
> 
Don't forget to use an appropriate subject line for your mails.
The criterium is the charge of the atom which is an option. If you don't 
like that you can use in index file saying which atoms are hydrophobic.

> 
> Thanks in adv.
> 
> Regards,
> Jian
> 
> -----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
> dynamics
> 
> 
> 
> 
>> 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
> dynamics
>> Date: Mon, 27 Aug 2007 09:18:30 -0400
>>
>> Thank you, Berk, for clearing it up for me.  I thought that maybe I
> didn't
>> understand something fundamental to the method.  The formula lacking
> the 
>> 1/T
>> 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
> calculation
>> automatically.
>>
>> -Steve
> 
> It's probably the same piece of latex formula that I just cut and pasted
> 
> several times.
> Shame on me for not checking better...
> 
> Berk.
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se