Try the representation: all not water Then set it to the HBONDS And refer to the VMD mailing list next time! :)
Jan ________________________________________ From: [email protected] [[email protected]] on behalf of Justin A. Lemkul [[email protected]] Sent: Friday, February 24, 2012 9:50 PM To: Hovakim Grabski; Discussion list for GROMACS users Subject: Re: [gmx-users] HBonds with VMD Hovakim Grabski wrote: > > > Dear GROMACS users, > I'm a novice user, > I've been trying to find a way to visualize hydrogen bonds with VMD,but > I haven't been successful. > After running a simulation of 13 Hypericin molecules solved in Water, I > loaded the.gro file and then the trajectory file .xtc, after that in the > Create Representation window I changed to CPK and then modified to show > just the Hypericin molecules (not water).Later I created another > representation and changed to HBONDS and in the panel changed to "name > H O",but VMD doesn't show the HBONDS formed between O and H atoms. > Where is my mistake? Probably the atom names are wrong. This is a VMD question, so you're better off posting to the VMD mailing list for help on such topics. -Justin -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! 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/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! 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/Support/Mailing_Lists
