From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Feb 09 2012 - 21:09:54 CST

On Thu, Feb 9, 2012 at 9:15 PM, Paymon Pirzadeh <ppirzade_at_ucalgary.ca> wrote:
> Hello,
> I am using VMD on Linux Ubuntu.
> I am trying to analyze the g(r) of the oxygen water molecules in the 10A
> vicinity of certain residues. This analysis is done on a GROMACS xtc
> file.
> In the gofr module, I am providing the following selections:
>
> Selection 1: name OW and within 10 of resid 10 11 14 15 16 17 19 20 21
> 22 42 45
> Selection 2: name OW and within 10 of resid 10 11 14 15 16 17 19 20 21
> 22 42 45
>
> So, I want to calculate the gofr for OW-OW among these water molecules.
> I check the 'update the selection' as well since these water molecules
> change with time. However, the resulting gofr is not properly normalized
> to 1 at large r. How can I trim the plot?

why should this pair distribution go to 1.0?

the limit of 1.0 only applies to *homogeneous*
atomic systems throughout the entire volume,
and due to the "within" it is not.

there is no way to determine the normalization
for anything but the entire volume anyway, since
the volume of a subsystem is an ill-defined property.

axel.

> Best,
>
> Paymon
>

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.