hi, I try to analyze H-bonds in an MD trajectory. when i look at the definition of an H-bond used by g_hbond it appears that only three atoms (acceptor, donor, hydrogen, ADH) are used in the analysis performed by this program ... however, i would assume that in fact 4 (or up to 6) atoms should be considered because the existence and the strength of an H-bond not only depend on the A-D distance and the ADH angle but also on the orientation of the lone pairs of the acceptor, and the latter are actually determined by the geometry of the atom(s), call them X, the acceptor is covalently bound to, aren't they?
So, in short, my question is: is anybody aware of a tool that can analyze the H-bonds in MD trajectories considering not only A-D distance and ADH angle but also the position of X (basically the dihedral DHAX) ? thanks for any hints cheers, michael -- View this message in context: http://gromacs.5086.x6.nabble.com/H-bond-analysis-tp5015899.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
