[gmx-users] Spatial distribution

[Justin Lemkul]

On 3/10/14, 6:35 AM, Norbert GARNIER wrote:
> Dear users,
>
> I have performed a coarse grain molecular dynamics simulation (MARTINI)
> to study the association of two identical alpha helix H1 and H2.
> I would like to analyse the spatial distribution of one helix arround the other
> and make a 2D representation as in Mark S. P. Sansom, Biochemistry 47, 40 2088
> figure 5.
> How can I do?

Looks like something g_densmap can do.  Since the authors report that they did 
all their analysis in Gromacs, if it's not straightforward how to do it, it's 
most efficient to contact the corresponding author and ask for advice in 
repeating the analysis.

-Justin

> Thank you very much for your help.
>
> Norbert Garnier
>
>

-- 
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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 601
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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