On 1/6/15 4:24 AM, Kester Wong wrote:
Dear Justin and all,
*보낸사람* : Justin Lemkul <jalem...@vt.edu>
*받는사람* : <gmx-us...@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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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