[gmx-users] radius of gyration - compactness - accessible surface area

[shahab shariati]

Dear Tsjerk

very thanks for your useful guidance.

I now know that I should compare output of g_gyrate (containing Rg vs time)
by area.xvg output file of g_sas (containing area vs time).

In area.xvg output file, there are several columns: "Hydrophobic",
"Hydrophilic" and "Total".

for example in time, 100 ps:

100    35.9501     60.9389     96.8891

area is in nm2.

from above number I understand that 35.9501 nm2 of area of protein that is
accessible to solvent belongs to
hydrophobic part of protein.

and 60.9389 nm2 of area of protein that is accessible to solvent belongs to
hydrophilic part of protein.

is my understanding true?

any help will highly appreciated.
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