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

[Justin Lemkul]

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.

>
> 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
> z-direction),
>
> 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:
>
> System
>
> Graphene (my substrate)
>
> Water
>
>
> 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
> density.xvg?
>

Yes.  But again, g_density is probably not what you want here; see the help 
description.

-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

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