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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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