VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Mar 10 2006 - 10:52:38 CST

Dear Michel,
you can use the attached script for this. To use it, source the script
and then run

getrad_overtime rmax seltext outfile

What it will then do is go through your trajectory and for each frame
output to outfile the mass of atoms contained in one angstrom radial
increments between 0 and rmax of atoms that correspond to what would be
selected by seltext (for example, "protein"). You can then do whatever
norming you see fit on this data (for example, averaging over frames or
norming by 1/r^2).

Best,
Peter

L. Michel Espinoza-Fonseca wrote:

>Hi all,
>
>I would like to know if any of you have developed a script to
>calculate the radial distribution for water and ions around a protein,
>using VMD.
>
>Thank you!
>Michel
>
>