[gmx-users] Hydrogen bonds

Dr. Seema Mishra seema_uoh at yahoo.com
Sat Jul 4 09:08:19 CEST 2015

 Thanks, I will try this option too. But now I would want to look at the particular hydrogen bonds between protein and ligand if these h bonds are present after the simulations. So, please let me know how can I interpret this data that I sent? ---

     On Saturday, 4 July 2015 11:49 AM, soumadwip ghosh <soumadwipghosh at gmail.com> wrote:

  the -hbn option in g_hbond in connection to your issue of determining
the hydrogen bond lifetime or stability does not tell you much. What you
should be looking at is running the g_hbond with -ac flag which gives you
the lifetime and H-bond formation energy between two groups specified by
you in the index file using either a predetermined or the default distance
and angle cut-off. GROMACS  obeys the Luzar and Chandler description of
H-bond kinetics which considers the H-bonds labile and the lifetime of the
same is calculated from the rate constants of H-bond breaking and

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-request at gromacs.org.


More information about the gromacs.org_gmx-users mailing list