[gmx-users] inquiry about SAS

Turgay Cakmak turgaycakmak34 at gmail.com
Tue Jul 3 16:49:06 CEST 2012

Hi all,

I am calculating SAS using g_sas of my system (several peptides in
water and ions, Na and Cl). I choose:
         for calculation group: non-water
         for output group: protein
 (400 out of 750 atoms were classified as hydrophobic)

When I plot the Area vs time graphs, both the hydrophobic-SAS and
hydrophilic-SAS decrease over the time. I think, the reason of the
hydrophobic-SAS decrease from 65 nm2 to 30nm2 is due to aggregation of
the peptides. But, I couldn't understant why hydrophilic-SAS is
decreasing from 40 nm2 to 20nm2 over time. Do the results make sense?

May be I mis-understand the meanings of the hydrophobic and
hydrophilic SAS. Please, someone could explain it to me, I would be so



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