From: Axel Kohlmeyer (
Date: Fri Feb 24 2017 - 15:12:28 CST

On Fri, Feb 24, 2017 at 3:47 PM, Tyler Westland <>

> I have a simulation that I must used topo readvarxyz to load into VMD.
> This is due to some of my molecules are switching between boxes. I am
> attempting to use gofr to

​i don't get your reasoning. ​are the total number of atoms not the same in
these cases? and if not, how come?

> calculate the radial distance of this molecule. When I use gofr on a
> single frame everything looks as expected. When I use gofr on two or more
> frames the data implies all the molecules have distance very close to 0. My
> question is what does gofr do to combine data between multiple frames, and
> if possible, why does this create what I am using.

​measure gofr computes the g(r) for each frame with the given volume
according to the selection.

topo readvarxyz does not preserve the identity of atoms, so any kind of
complex selections based on what belongs to one or another molecule cannot

​the total g(r) for multiple frames is just the average over all individual
g(r)​ for each frame. you could achieve the same by doing a loop and only
processing one frame at a time. if i was in your situation (and if there is
not some other principal issue, that you have not mentioned), i would
probably split the .xyz file and process each as a separate molecule and
collect and average the g(r) from those.


> Tyler Westland

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.