[gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 15
jalemkul at vt.edu
Thu Dec 4 13:54:03 CET 2014
On 12/4/14 6:54 AM, soumadwip ghosh wrote:
> Dear Alex,
> as you can see in my previous mail, I have made groups in the
> index files using make_ndx (gp no 10-17). My question is with the kind of
> groups I have, how can I calculate H bonding between chain A and chain B in
> presence of sodium . Should I merge gp 13 and 2 together and make a gp (say
> 18) and then use g_hbond for groups 18 and 14? i
The presence of sodium has no implication on the calculation of hydrogen bonds,
as it serves neither as a donor nor acceptor for hydrogen bonding. To examine
hydrogen bonding between two chains, all you need is two groups with the atoms
of interest in each.
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
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