[gmx-users] number of solvent molecule

[Erik Marklund]

The -num output (non-optional I think) shows the number of (for
instance) solvent molecules within distance r at each frame. Is that not
exactly what you are trying to find out? r = 0.35 nm by default, but may
be set to 0.6 with the -r flag. Now, disregard what I wrote in my last
mail, because you DO want to use the -contact flag since it allows
analysis of non-hydrogen-bonding atoms.

On Tue, 2006-11-28 at 18:08 +0000, chiradip chatterjee wrote: 
> 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.

Isn't it? I do not see the difference, since contact means 'within
distance r', r being 0.6 nm in your case. What is your solvent by the
way?

>  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 
> _______________________________________________
> 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