[gmx-users] regarding the use of g_hbond

Justin Lemkul jalemkul at vt.edu
Fri Dec 18 16:19:42 CET 2015

On 12/18/15 5:42 AM, soumadwip ghosh wrote:
> Hi all,
>          I am trying to plot the no.of hydrogen bonds between two parallel
> chains of a double stranded DNA as a function of time. What I am observing
> is a decrease (which is expected) for two types of nucleic acids but the
> problem is the difference between three or more data are difficult to
> visualize due to large data points. I want the plot to look something like
> FIG 6 of the following reference below
> http://scitation.aip.org/docserver/fulltext/aip/journal/jcp/136/6/1.3682780.pdf?expires=1450435942&id=id&accname=2102180&checksum=AC45165AFD6BC0C361795C50AED25E13

This link is broken.

> where the difference is clearly observed. However what I am getting from
> GROMACS 5.0.5 and Origin software is something as follows
> https://drive.google.com/file/d/0B7SBnQ5YXQSLYUxiSk9aRVIwbzg/view?usp=sharing
> Is there any workaround to achieve what I am looking for?

Your data seem pretty clear as they are.  Perhaps try plotting as a running 
average to remove some of the fluctuation.



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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