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

[Justin Lemkul]

On 12/31/14 6:48 AM, Kester Wong wrote:
> Dear Justin and all,
>
>
>
> I am stoked by what g_select can do (after reading the gmx-users list) and there
> is no one-size-fits-all.
>
> However, as I wanted to look for more resources on g_select, I was met with no
> further information, for example:
>
> g_select_mpi -select 'help position' OR g_select_mpi -select 'help all'
>
> The commands below did not return anything but "No trajectory or topology provided, nothing to do!".
>

Seems like the old syntax doesn't work.  You may want to start a new thread 
specifically asking about g_select to draw attention to this issue.

-Justin

>
>     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.
>
>
> Firstly, I am only able to use g_select to define the bottom bin for water
> droplet; could you please advise on indexing the bins from the bottom water layer?
>
> g_select_mpi -f traj_comp.xtc -s topol.tpr -n system.ndx -b 9000 -e 10000
> -select 'resname SOL and res_com z < 10' -on output-system.ndx
>
>
> How does one select SOL between z > 10 and z < 15, so on and so forth?
>
> I have looked at this for
> reference: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-June/072150.html
>
>
>
> I am aware that after g_select, I will also have to do the following
>
> - Perform center of mass calc to identify the relative position of the droplet:
> g_traj -f traj_comp.xtc -s topol.tpr -n system.ndx -com -fp -b 9000 -e 10000 -ox
> coord.xvg
> - Suppose there are more than one frame within the 9-10ns period, a shell script
> will be needed to loop through the frames for the (R,z) extraction?
>
> One must then use a shell script to conduct further analysis using the produced
> index files, something like your script below?
> https://www.mail-archive.com/gmx-users@gromacs.org/msg52656.html
>
> Thanks for your advise and I wish you a jolly 2015!
>
> Regards,
>
> Kester
>
>
>
>
>
>
>     >
>     > 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
>
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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 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

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