[gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 15

[Justin Lemkul]

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

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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
http://mackerell.umaryland.edu/~jalemkul

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