[gmx-users] number of solvent molecule
chiradip75 at yahoo.co.uk
Tue Nov 28 23:59:03 CET 2006
thanks for ur reply. But could you please tell me the
command to integrate the rdf to first maximum. I
searched for it and did not find any thing and why I
double the value?.
--- chris.neale at utoronto.ca wrote:
> > 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
> > the no of molecule present. Is there any
> > 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
> >> flag if you feel
> >> like it. In any case, g_hbond is probably the way
> >> 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
> >> 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
> >> of my
> >> > > protein in a solvent box.
> >> > > Now I want to calculate the number of solvent
> >> > > molecules (molecules/cc) present arround a
> >> of
> >> > > 0.6nm from my protein (or sidechains).
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