[gmx-users] number of solvent molecule

[chiradip chatterjee]

Hi Erik
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

--- Erik Marklund <erikm at xray.bmc.uu.se> wrote:

> 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).
> > > Please help me.
> > > Thanks in advance
> > > Chiradip Chatterjee
> > > 
> > > Chiradip Chatterjee 
> > > Post Doctoral Research Associate 
> > > Department of Chemistry and Biochemistry 
> > > University of California, Santa Barabara 
> > > USA
> > > Phone:1-805-6859381 
> > > Mobile :1-805-637-7995
> > > E-mail:chiradip75 at yahoo.co.uk 
> > >        cchatterjee at chem.ucsb.edu 
> > > Home Page: www.chem.ucsb.edu/~cchatterjee/ 
> > > Group home page : www.chem.ucsb.edu/~gerig/
> > > I LOVE KOLKATA
> > > 
> > > Send instant messages to your online friends
> http://uk.messenger.yahoo.com 
> > > _______________________________________________
> > > 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
> -- 
> Erik Marklund, PhD Student, Molecular Biopcysics
> group,
> Dept. of Cell and Molecular Biology, Uppsala
> University.
> Husargatan 3, Box 596,          75124 Uppsala,
> Sweden
> phone: +46 18 471 4537          fax: +46 18 511 755
> erikm at xray.bmc.uu.se
> 
> _______________________________________________
> 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
> 


Chiradip Chatterjee 
Post Doctoral Research Associate 
Department of Chemistry and Biochemistry 
University of California, Santa Barabara 
USA
Phone:1-805-6859381 
Mobile :1-805-637-7995
E-mail:chiradip75 at yahoo.co.uk 
       cchatterjee at chem.ucsb.edu 
Home Page: www.chem.ucsb.edu/~cchatterjee/ 
Group home page : www.chem.ucsb.edu/~gerig/
I LOVE KOLKATA

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