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
--- [EMAIL PROTECTED] 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 [email protected] > 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 > Send instant messages to your online friends http://uk.messenger.yahoo.com _______________________________________________ gmx-users mailing list [email protected] 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
