[gmx-users] number of solvent molecule

[chiradip chatterjee]

Hi Chris.
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?.
Chiradip

--- 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
> 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).
> 
> >
> 
> 
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the
> list. Use the
> www interface or send it to
> gmx-users-request at gromacs.org.
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> 


Send instant messages to your online friends http://uk.messenger.yahoo.com