VMD-L Mailing List

From: Robert Johnson (robertjo_at_physics.upenn.edu)
Date: Tue Jun 18 2013 - 11:43:13 CDT

Hello All,
I'm developing some exercises on simulating Lennard-Jones fluids as part of
a lab for introductory physics courses. The goal is to compare a
Lennard-Jones fluid to an ideal gas. Students will investigate
freezing/boiling (qualitatively) and calculate the equation of state
(pressure vs. temperature at several fixed densities). Since this is meant
to be very introductory, I've written a bunch of TCL scripts that automate
setting up the system and launching a NAMD simulation from VMD.

A possibility that I'm investigating is using the AutoIMD feature in VMD.
However, since I'm interested in calculating the pressure for each
simulation, I would like to use periodic boundary conditions. Is it
possible to use periodic boundary conditions with AutoIMD? Another
possibility would be to enclose the system in a box and freeze the box
atoms within AutoIMD. However, I'm not sure how I would extract the
pressure of such a system.

Another possibility would be to launch the simulation and have VMD simply
update the frame on the fly so that users can watch the simulation
progress. Is this possible?
Thanks,
Bob 

-- 
Bob Johnson, PhD
Lab Coordinator & Lecturer
Department of Physics and Astronomy
University of Pennsylvania
209 S. 33rd St.
Philadelphia, PA 19104
Office: David Rittenhouse Laboratory 2C11
Phone: 215-898-5111
http://www.physics.upenn.edu/~robertjo