VMD-L Mailing List

From: Paymon Pirzadeh (ppirzade_at_ucalgary.ca)
Date: Thu Feb 09 2012 - 20:15:15 CST

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?
Best,

Paymon