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

[Tsjerk Wassenaar]

You understand correctly.

On Tue, Jun 21, 2011 at 11:35 AM, shahab shariati
<shahab.shariati at gmail.com> wrote:
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands