[gmx-users] g_sas

[Cheong Wee Loong, Daniel]

Thanks Justin for the reply.  I did read the help and manual and understand that the output file can be the whole or part of the calculation group.  What I don't quite understand is what the output group represents. I am assuming that the calculation group would be the group of atoms that will be probed to determine the solvent accessible are.  If so, what does the output group represent?

Thanks.


-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul
Sent: Thursday, April 23, 2009 6:26 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_sas



Cheong Wee Loong, Daniel wrote:
> Dear all,
>
>
>
> I am interested to calculate the hydrophobic and hydrophilic area of the
> surface of the protein layer I am simulating.  It looked like g_sas
> would be able to give me what I was looking for.  But I was wondering
> what the difference is between the calculation group and the output
> group.  In particular, what is the output group?  I tried looking in the
> manual and in the archives but I can't seem to find an answer to it.
>

 From g_sas -h:

"The calculation group should always consists of all the non-solvent atoms in
the system. The output group can be the whole or part of the calculation group."

-Justin

>
>
> Thanks.
>
>
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--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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