VMD-L Mailing List
From: Philippe Bopp (philippebopp_at_yahoo.com)
Date: Fri Mar 21 2014 - 12:21:38 CDT
in a periodic system with periodicity L (=20 A in your case)
it is not meaningful to compute g(r) for r > L/2
depending how you 'pack' your atoms 'uniformly', you may have unphysical
overlaps between particles and your g(r) will look weird (and not =0)
at short distances 9and will thus possibly also be distorted at larger
I tried to use the extension g(r). I have a trajectory of a system which packs simple one atom in the 20x20x20 (unit length) periodic box. As instructed on the plug in webpage, I set the unit cell dimension using the Utilities. I have checked the Use PBC in the options. My selection 1 and selection 2 are both "name W", which is my name of atom uniformly distributed in the system. I put max.r as 20.0.
The output RDF figure looks right. However, the profile is truncated around r=14. To be more specific, I have a range of r around the value g(r)=1, but g(r) becomes zero at 14.3 to 20.0. Shouldn't I have all g(r)=1 to the boundary of periodic box r=20? Would you please indicate wherever I did it wrong? Thank you.
-- Ming-Tsung Lee Department of Chemical & Biochemical Engineering Rutgers, The State University of New Jersey 98 Brett Road, Piscataway, NJ 08854-8058