[gmx-users] hydrogen bond analysis

[Justin Lemkul]

On 6/19/17 3:49 AM, João Henriques wrote:
> Dear Imrul,
> 
> I believe the information you seek is right there in your xvg file header:
> 
> @    xaxis  label "Time (ns)"
> @    yaxis  label "Number"
> 
> ...
> 
> @ s0 legend "Hydrogen bonds"
> @ s1 legend "Pairs within 0.35 nm"
> 
> First column is always time (x-axis). All other columns are y-axes for
> different properties (in this case you two, s0 and s1). s0 is clearly
> stated as being hydrogen bonds and s1 as pairs within 0.35 nm.
> 

Just to add on: pairs within 0.35 nm are pairs of atoms that satisfy the 
hydrogen bonding distance criterion, but not the angle.  The two columns in the 
output file are mutually exclusive (see lots of discussion from last week on 
this same topic).

-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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