[gmx-users] g_hbond/g_sas - how is it calculated?

[lina]

On Wed, Jun 8, 2011 at 10:20 PM, Marzinek, Jan
<j.marzinek10 at imperial.ac.uk> wrote:
> Hi,
>
>
>
> I have a question related to the calculation of hydrogen bonds in Gromacs.
> As I read in Manual it comes from the distance between donor and acceptor (
> <= 0.35 nm) and the angle <=30 degr beween hydrogen and acceptor. The
> question is - why 30 degr? How is it related to the reality?

It's a default value, you can change it when you need.

>
>
>
> The second thing is the claculation of the accessible surface area
> (g_sas) of the molecule for instance? It is not explained in manual and I am
> really curious how g_sas makes these calculations.
>
> As my supervisors do not know the gromacs their questions are always about
> such details :)
>
> However, I think it is really important to understand what you are really
> doing using commands in Gromacs which provide you with really detailed
> results.

All I can say is that, practice and problems are a good teacher.

>
>
>
> Thank you in advance,
>
>
>
> Jan
>
>
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-- 
Best Regards,

lina