[gmx-users] Re: How to countting Hbonds lifetime

Justin A. Lemkul jalemkul at vt.edu
Thu Feb 24 15:33:56 CET 2011

gromacs564 wrote:
>  Hi  Justin
>  What is your means that "the HBond's  occupancy "? Can you tell me the 
> difference about Hbonds lifetime and occupancy?

The script I wrote simply counts the number of times a certain hydrogen bond 
appears in the output that g_hbond already gives you and reports it in a 
convenient percentage, that's it.  There are no kinetics or energetics implied. 
  g_hbond can calculate hydrogen bond lifetimes, the references for which are 
printed by the program.  I'd suggest you read them.

> I want to know which residues form the Hbond and the donor-acceptor atoms.
> The g_hbond can do it?

Sure, that's what hbond.ndx and hbmap.xpm are.


>    Thank you very much.


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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