Part 2: Molecular Dynamics
In this part of the workshop you have seen how to perform molecular dynamics simulations using namd. namd is one of many highly capable molecular dynamics programs, all of which have similar features and configuration parameters. All modern molecular dynamics programs provide SHAKE (or a variant) to constrain the lengths of bonds involving hydrogen. All provide an implementation of periodic boundary conditions and all provide PME (particle mesh Ewald) to model long range electrostatic interactions. All provide thermostats and barostats that can be used to run simulations at constant temperature and pressure.
Your choice of molecular dynamics program is as personal as your choice of molecular viewing program. All programs are highly capable and efficient. In my opinion, namd is the easiest to learn and use on a local desktop computer, GROMACS is the fastest (free) program that scales well from 10’s to 1000’s processors on a supercomputer cluster, and pmemd.cuda (part of AMBER, and not free) provides the fastest molecular dynamics program that runs on a GPU (graphics processor).
If you want to move beyond what you have learned in this part of the workshop, then each of the above programs come with complete documentation and tutorials. Otherwise, feel free to take a break now while you wait for your molecular dynamics simulation of zanamivir bound to H7N9 neuraminidase to complete, before moving onto the next part of the workshop.