[gmx-users] H-bond query

Justin Lemkul jalemkul at vt.edu
Fri May 22 22:21:51 CEST 2015

On 5/22/15 9:19 AM, soumadwip ghosh wrote:
> Hello all,
>               I am trying to see what happens to the no. of
> Watson-Crick hydrogen bonds between two parallel chains of a double
> stranded DNA on incorporating a flat graphene sheet. The no of
> interchain H-bonds are supposed to decrease with time. But I am not
> sure how to use g_hbond in order to demonstrate this. How should I
> make index groups for the two chains of DNA? Should I take all the
> atoms into account (except backbone) and then index them like chain_A
> and chain_B and then analyze the hbnum.xvg file from g_hbond?
> Furthermore, in the hbnum.xvg file the third column represents the no.
> of H-bond within the distance cut-off and the 2nd one is the total no
> of hydrogen bonds as a function of simulation time. So, which one
> should I plot in this case against time?

You probably care about the actual H-bonds, not the atom pairs that are within 
distance but don't satisfy the angle criterion.  Watson-Crick hydrogen bonding 
is a very straightforward definition; the index group should be straightforward. 
  For anything else that comes up in a melted state, well, that's up to what 
you're seeing and what you're interested in.



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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