[gmx-users] How to plot a droplet radius profile as a function of z-direction?
jalemkul at vt.edu
Sat Dec 27 15:55:46 CET 2014
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:
> 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
> Q2) Another question that I have is, suppose I have equilibrated (NVT) a water
> droplet for 10ns, and would like to plot the H-bond density (along the
> I type the following command:
> g_density_mpi -f traj_comp.xtc -n system.ndx -s topol.tpr -b 9000 -e 10000 -sl
> 1000 -dens number -o number-density-OH.xvg
> I was only able to select:
> Graphene (my substrate)
> How can I create a system.ndx such that it allows me to choose the OH (instead
> of water)?
make_ndx or g_select create index files. If you're defining "hydrogen bond
density" as "number of hydrogen bonds per slice," along with the above, you need
g_select and then you need g_hbond. g_density is not the right program here.
> Q3) Regarding Q2, the g_density_mpi utility read the frames contained within the
> time frame of 9 - 10 ns, but does it average the frames to give a time-averaged
Yes. But again, g_density is probably not what you want here; see the help
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
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