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

Justin Lemkul jalemkul at vt.edu
Thu Nov 22 19:02:21 CET 2012

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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