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 <[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