From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Oct 23 2019 - 15:49:48 CDT

i don't see any cell dimension information here.
this is an .xyz file, right?
those only store positions, not cell information.

axel.

On Wed, Oct 23, 2019 at 12:57 PM Sarah Fowler <sueyfowler_at_gmail.com> wrote:

> I would like to plot RDFs for molecular dynamics simulation results. The
> simulations ran in the NPT ensemble. This means that I can't use VMD's GUI
> for plotting RDFs available at Extensions/Analysis/Radial Pair Distribution
> Function. I have a different cell volume/parameter at each time step, but
> the GUI only allows a single cell volume.
>
> I have spent a couple of months trying to find other software that can do
> this and have had no success, either because I can't access software that
> can do it or it has not been possible to find out how to do what I need.
>
> Does anyone know if there is a way to do this in VMD? I am stuck. If
> there is, I would be very grateful for any newbie-level advice. I have two
> relevant files. (1) My cell volume/parameter files are in XYZ format
> (three columns) and my cells have 90 degree angles. (2) My trajectory
> files have the following format:
>
> 1000
>
> i = 0, time = 0.000, E = -1862.5354785273
>
> Mg 2.7122680189 11.0569574242 6.8765696187
>
> Mg 1.7122680189 7.0569574242 2.8765696187
>
> Mg 9.8778827417 5.5336942397 3.4088988234
>
> Thank you.
>

-- 
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.