Eva Riveira: Classical Molecular Dynamics with VMD/NAMD

In this tutorial we will go over the usage of VMD and NAMD to run classical molecular dynamics
simulations, specifically for membrane systems. We will try to cover the basics for setting up a system
in VMD, running MD in NAMD and using the two programs for some elementary analysis. The
tutorial will be given in three parts as follows:

1) Preparing the system in VMD
A. Topology files
B. Protein preparation
C. Adding the membrane
D. Solvating the system

2) NAMD
A. Preparation of files
B. Flags – output, cutoffs, electrostatics, etc.
C. Minimization and equilibration

3) NAMD cont.
A. Standard output
B. Using NAMD with VMD for analysis