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 <[EMAIL PROTECTED]> 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:[EMAIL PROTECTED] > > > > [EMAIL PROTECTED] > > > > 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@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 > > [EMAIL PROTECTED] > > > > 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 > > [EMAIL PROTECTED] > > > > _______________________________________________ > > gmx-users mailing list gmx-users@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 > > [EMAIL PROTECTED] > > 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:[EMAIL PROTECTED] > [EMAIL PROTECTED] > 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@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 [EMAIL PROTECTED] > 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 [EMAIL PROTECTED] _______________________________________________ gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php