[gmx-users] g_hbond

Justin Lemkul jalemkul at vt.edu
Fri Jul 10 03:05:01 CEST 2015

On 7/9/15 9:02 PM, Nilesh Dhumal wrote:
> Hello,
> I am calculating g_hbond for water system.  I have a question about
> specifying two group for calculating hydrogen bond.
> Do I specify atoms in triplet(O-H---O)?
> Can I specify O-H as one group (Donor-Hydrogen) and O in other group
> (Acceptor)?

If the system is pure water, you do not need any special index groups.

> Default  -r cutoff is 0.35nm. Is the distance between hydrogen---acceptor
> or distance between donor---acceptor?

Read the first sentence of the help description.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


More information about the gromacs.org_gmx-users mailing list