I went through the documentation of g_hbond, But I
think it does not give me the number of solvent
molecules present in a solvent shell arround my
protein. I am able to calculate no. of contacts
between protein and solvent but that is not equal to
the no of molecule present. Is there any suggetion?
regards
Chiradip
Use g_rdf and integrate the radial distribution function to either
a)the first minimum
b)the first maximum and double the value
c)some predetermined cutoff value (like 0.6nm, athough that sounds a
little large to be a single solvation shell).
Come to think of it, you can even skip the -contact
flag if you feel
like it. In any case, g_hbond is probably the way to
go. Have a look at
its documentation.
/Erik
On Tue, 2006-11-28 at 09:43 +0100, Erik Marklund
wrote:
> g_hbond -contact. But then again, that's my answer
to everything :-)
>
> Oh, and use (one of) the latest versions of
gromacs, otherwise the
> -contact option might not work properly.
>
> /Erik
>
> On Mon, 2006-11-27 at 21:14 +0000, chiradip
chatterjee wrote:
> > Hi gmxusers,
> > I am a new user of gromacs. I completed a MD run
of my
> > protein in a solvent box.
> > Now I want to calculate the number of solvent
> > molecules (molecules/cc) present arround a shell
of
> > 0.6nm from my protein (or sidechains).
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