[gmx-users] hbond analysis

[Justin Lemkul]

On 11/4/14 7:26 AM, Urszula Uciechowska wrote:
> Dear Gromacs users,
>
> Regarding the g_hbond analysis.
> What does exactly represent the second and third column in hbond.xvg file
> (pasted below)?
>
>
>   g_hbond is part of G R O M A C S:
> #
> # Gromacs Runs One Microsecond At Cannonball Speeds
> #
> @    title "Hydrogen Bonds"
> @    xaxis  label "Time"
> @    yaxis  label "Number"
> @TYPE xy
> @ view 0.15, 0.15, 0.75, 0.85
> @ legend on
> @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ s0 legend "Hydrogen bonds"
> @ s1 legend "Pairs within 0.35 nm"

As the legends say, the data presented are hydrogen bonds, and then pairs of 
atoms that are within the distance criterion but do not satisfy the angle 
criterion for being a hydrogen bond.

-Justin

>           0           0           0
>           1           0           0
>           2           0           0
>           3           0           0
>           4           0           0
>           5           0           0
>           6           0           0
>           7           0           0
>           8           0           0
>           9           0           0
>          10           0           0
>          11           0           0
>          12           0           0
>          13           0           0
>          14           0           0
>          15           0           0
>          16           0           0
> :
>
> Best regrads
> Urszula
>
>
> University of Gdansk and Medical Univesity of Gdansk
> Department of Molecular and Cellular Biology
> ul. Kladki 24
> 80-822 Gdansk
> Poland
>
>
> -----------------------------------------
> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
> http://www.ug.edu.pl/
>

-- 
==================================================

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

==================================================