VMD-L Mailing List

From: Sarah Fowler (sueyfowler_at_gmail.com)
Date: Wed Oct 23 2019 - 11:25:03 CDT

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.