VMD-L Mailing List

From: Kartheek (kartheek.p_at_research.iiit.ac.in)
Date: Sat Sep 03 2011 - 12:49:00 CDT

Sorry for that,Here i am providing all the information.

-VMD for linux 1.9
-ubuntu 11.04
-selection1:name O1P Selection2:name OH2
-I am doing salvation of RNA by using vmd only.
 in order to check my analysis, I performed 10 ns simulation of water box having 233 water molecules which was generated by using vmd.
For the water box system, I tried to plot RDF.
 selection1:name OH2 selection2:OH2
for this system also i am getting similar plots.
Thank you
----- Original Message -----
From: "Axel Kohlmeyer" <akohlmey_at_gmail.com>
To: "Kartheek" <kartheek.p_at_research.iiit.ac.in>
Cc: vmd-l_at_ks.uiuc.edu
Sent: Saturday, September 3, 2011 9:50:33 PM
Subject: Re: vmd-l: Radial distribution function

This is a useless report, since you don't provide _any_ way to
reproduce this. You have to provide the following:
- which version of VMD you are using
- which platform you are running on
- which selection texts you are using
- whether you get this behavior only with you data or, for example
also when using the salvation water box that ships with VMD
- ideally access to you data set, so that the situation can be
debugged further, in case it is specific for your data

Cheers,
      Axel

On Sep 3, 2011, at 9:12 AM, Kartheek <kartheek.p_at_research.iiit.ac.in> wrote:

> Hi All,
> I am trying to calculate RDF of a system having nucleic acid in water box,I used VMD built in plugging to plot RDF of Oxygen atoms of nucleic acid back bone VS Oxygen atoms of water.
> The plots which it generating doesn't make any sense to me,i tried with different phrase selections, what ever may be the phrase selection it is giving same plots only.Here I am providing an URL for the plot.
> Thanks in advance.
> http://researchweb.iiit.ac.in/~kartheek.p/rnagr.jpg