[gmx-users] G_sas change in hydrophilic and hydrophobic surface area

[Justin Lemkul]

On 11/22/12 2:36 AM, rama david wrote:
> Dear user ,
> I simulate the two  protein in random coil position, when they come close
> they form antiparallel  beta sheet structure.
>     I want to calculate the change in hydrophilic and hydrophobic surface
> area over my simulation time.
> For usig g_sas  Should I have to make the different index group for
> hydrophilic and hydrophobic residues
> Or should only have to select the option protein both the time.
>

The whole protein should always be the group for the surface calculation. 
Whatever subset of those atoms (i.e. residues of interest) can be the output group.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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