[gmx-users] radial distribution function

Mon Sep 19 01:36:11 CEST 2011

Does not really matter which one you load up, just one towards the end of the trajectory probably so you can be sure it is selected from the "equilibrium" state of the system.

Then type "2" when over the  display window with VMD, then click on two atoms.  VMD will then display a line between the two atoms with a distance in Angstroms.  What you want to do is try and work out what the radii mean in the polymer system.  It will correspond to a particular structure and arrangement of the atoms.  You need to do this with any RDF, so that you can actually work out what the peaks actually mean.

The other option is to use a transparent sphere representation of a couple of the particular atom types, and adjust it's radius to the various peaks, this should make it much easier for the visualisation and identification of the structure associated with each peak.

Remember that VMD works in Angstroms and GROMACS in nm.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: Moeed [mailto:lecielll at googlemail.com]
Sent: Saturday, 17 September 2011 1:58 AM
To: Discussion list for GROMACS users
Cc: Dallas Warren; tsjerkw at gmail.com
Subject: Re: [gmx-users] radial distribution function

Thank you Dr Warren for your comment. I actually still need your help with your hint. I am not able to realize how to measure the distances..do I have to look at the plot and find the distance shown by the Peaks and then look at the same distance in VMD ? But which frames do I have to upload?

Please guide me a little more.

Thank you,
On Thu, Sep 15, 2011 at 6:26 PM, Dallas Warren <Dallas.Warren at monash.edu<mailto:Dallas.Warren at monash.edu>> wrote:
Load up some frames into VMD and start measuring the distances shown by the peaks in your RDF, link them with what you actually see in there (using something like a transparent representation of the carbon atom(s) using VDW then set the sphere scale so that it matches the correct radius, may be an easier way to do this, but this would make it easy to see).  Appears it may be something real, so just check the coordinate file and see where they are actually coming from.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu<mailto:dallas.warren at monash.edu>
+61 3 9903 9304<tel:%2B61%203%209903%209304>
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-bounces at gromacs.org<mailto:gmx-users-bounces at gromacs.org> [mailto:gmx-users-bounces at gromacs.org<mailto:gmx-users-bounces at gromacs.org>] On Behalf Of Moeed
Sent: Friday, 16 September 2011 12:55 AM
To: jalemkul at vt.edu<mailto:jalemkul at vt.edu>; Discussion list for GROMACS users
Subject: Re: [gmx-users] radial distribution function

Hello again,

I tried comparing RDF plots generated by sampling from 4 to 5 ns run and a longer run from 4 to 30 ns to see whether the small jumps on the plot are due to insufficient sampling. Attached is the new plot showing that two RDF curves are almost identical. I only wanted to let you know and please comment on the attached plot if you have any ideas. Thank you. :)

Moeed
On Sat, Sep 10, 2011 at 10:00 AM, Moeed <lecielll at googlemail.com<mailto:lecielll at googlemail.com>> wrote:
Thank you for your input. I am going to run for another 15 ns to see if the little jumps vanish.

Best,

On Fri, Sep 9, 2011 at 9:16 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:jalemkul at vt.edu>> wrote:

lina wrote:

On Sat, Sep 10, 2011 at 3:35 AM, Moeed <lecielll at googlemail.com<mailto:lecielll at googlemail.com> <mailto:lecielll at googlemail.com<mailto:lecielll at googlemail.com>>> wrote:

   Dear users,

   I have created radial distribution function plot for Carbon atoms in
   a system containing polymer chains. I see some little jumps between
   first and second peak.
   I need your help to comment on how this behavior can be justified
   (or if the plot is wrong).

   g_rdf -f *.trr -s *.tpr -o *.xvg -n *.ndx -b xxx
   Thank you in advance.

I think your figure is fine.

I think, based on information given in subsequent messages, that there is insufficient data collection to assess whether this RDF plot is as meaningful as it could be.  There is nothing glaringly wrong, but the roughness is due to insufficient sampling.

You just need how to proper interpret your figures, truly understand what the "radial distribution" means.

I think it inappropriate to suggest that the OP does not understand the concept behind the figure; some guidance, perhaps is necessary, but nothing more.

-Justin

--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu<http://vt.edu> | (540) 231-9080<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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