[gmx-users] How to plot a droplet radius profile as a function of z-directio

[Justin Lemkul]

On 1/6/15 4:24 AM, Kester Wong wrote:
> Dear Justin and all,
>
>
>
>     *보낸사람* : Justin Lemkul <jalemkul at vt.edu>
>     *받는사람* : <gmx-users at gromacs.org>
>     *받은날짜* : 2014년 12월 27일(토) 23:55:33
>     *제목* : Re: [gmx-users] How to plot a droplet radius profile as a function
>     of z-directio
>
>     On 12/27/14 2:05 AM, Kester Wong wrote:
>     > Dear gmx-users,
>     >
>     >
>     >
>     > Q1) I would like to plot the radius profile of a water droplet on graphene, as a
>     > function of z-direction, as per below:
>     >
>     > http://journals.aps.org/prl/article/10.1103/PhysRevLett.109.176101/figures/2/large
>     >
>     >
>     > Which GROAMCS utility should I use, and how do I go about plotting the profile?
>     >
>
>     It will require several steps.  Not something I've ever done, but I would think
>     g_traj for coordinate extraction, then post-processing to calculate the diameter
>     or radius, would be the first step.  Presumably you would have to do this for
>     various slices (assuming you're looking at cross-sections in the x-y plane for
>     varying values of z), so g_select to define atoms within that slice will be
>     needed before even running g_traj.  Then you construct the profile from this
>     information.
>
>
> I have selected the slices of water along the z-direction. I assume the next
> step would be using g_traj to extract the coordinates.
> How do I go from running g_traj to post-processing the droplet radius?
>
> Do I use this command as follows:
> g_traj -f traj_comp.xtc -s topol.tpr -n selected-bins.ndx -b 9000 -e 10000
> -nojump -fp -ox coord.xvg
>

Well, how do you define a circle?  Find the maximum and minimum coordinates 
along x and y, that's (roughly) your diameter...

-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

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

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