VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Mar 01 2012 - 17:36:46 CST

On Thu, Mar 1, 2012 at 5:38 PM, siladitya mukherjee
<mukherjeesiladitya_at_gmail.com> wrote:
> Hi,
>
> I am trying to calculate RDF from a xyz file in VMD, but the error I am
> getting is "error measuring gofr", unit cell volume is zero. I am using PBC
> for the calculation and also included the command pbc set {Lx Ly Lz}, so I

pbc set by default is applied only to the current
frame. you probably have to use the -all flag or do
a loop, if the cell volume changes and you
read the cell information from a file. or use the gui.

axel.

> specified my box lengths also which is required when I am using PBC in RDF
> calculation. I can't understand whether there is any other thing I need to
> do for calculating RDF from xyz file, because I got correct RDF by following
> the exact same procedure with mol2 and dcd files. Any help regarding this
> matter would be appreciated.
>
> Thanks,
> Siladitya 

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