From: Axel Kohlmeyer (
Date: Sat Sep 03 2011 - 16:25:05 CDT

On Sat, 2011-09-03 at 23:19 +0530, Kartheek wrote:
> 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

can you please try using the wat.pdb file instead
that ships with the solvate plugin in VMD?
the file is located in the VMD's "lib" directory
under "plugins/noarch/tcl/solvate1.4/wat.pdb

load the file, then do:
pbc set {65.4195 65.4195 65.4195}
and compute the g(r) for the water oxygens.

> for this system also i am getting similar plots.

the only way that i can imagine this would happen
is, if your system cell information is not correct.

i assume the trajectory looks otherwise ok,
when being visualized in VMD?
did you do any post-processing?
which MD software did you use and
which file format? is your system
cell orthogonal?


> Thank you

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.