VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Mar 21 2014 - 11:08:28 CDT

On Fri, Mar 21, 2014 at 11:23 AM, Ming-Tsung Lee <mtlee_at_rci.rutgers.edu> wrote:
> Version: VMD 1.9.1 on Windows 8.1 x64
> Function: VMD extension for radial pair distribution function
>
> Questions:
> 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.

you disregarded the fact that minimum image conventions apply for the
measure gofr command. you can only fit a sphere of 10 \AA _radius_ in
a 20x20x20 cubic box. measure gofr contains a "smart" normalization
function, that can also handle where you go into the edges (to max_r =
20*sqrt(1/2) ), but with less reliable statistics due to limited
number of pairs.

axel.

>
> Best Regards,
> --
> Ming-Tsung Lee
> Department of Chemical & Biochemical Engineering
> Rutgers, The State University of New Jersey
> 98 Brett Road, Piscataway, NJ 08854-8058
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.