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
glad.
Thanks,
Turgay
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