This directory contains a script intended both as a demonstration of use, and as a regression test.
It can be launched with
vmd -dispdev none regtest.tcl
On first run, the script will download ~250MB of simulation results part of the case study for the MEMBPLUGIN tool.
The simulation data corresponds to 20 ns of simulation of a 1:1 molar ratio POPC:Cholesterol bilayer. The bilayer was modeled at all-atom resolution with the CHARMM36 forcefield. The details of the system preparation are reported in the case study.
The script computes lateral MSD displacement for time intervals ranging from 2 to 10 ns for the POPC and Cholesterol species separately. Diffusion coefficients can be determined from asymptotic slopes of the curves (usually fitting linear models).