Introduction to Molecular Dynamics

This exercise is to familiarize yourself with CLAMPS, AtomViewer and the Analyzer programs. It will also deal with constant temperature simulations with a Nose thermostat.

1. Change to the clamps directory and run CLAMPS. The run id is ex1, and it should produce the output files ex1.out, ex1.crd, and ex1.sca. (The input file can also be downloaded: ex1.in)

   This input file is in 2 dimensions and has 16 particles.

   • Look at the configurations in ex1.crd with the AtomViewer, which will show an animation of the simulation. To run the AtomViewer, type atomviewer ex1.crd.
   • Look at the scalar data with the DataSpork, which will show a trace of a selected variable, along with some error analysis. Run DataSpork by typing dataspork, and open the files using the File/Open Datasets menu.

2. Starting from the previous ex1.in file, change it to run at a temperature of kT=1 and a density of 0.3 (all using reduced units so that eps=1, sigma=1). You may want to refer to the main CLAMPS page and look at the keyword descriptions to understand the input file.
   • Determine the largest timestep one can use and still get energy conservation better than 1% of the kinetic energy fluctuations.
   • How quickly does the kinetic energy relax to equilibrium? How do you decide that it has equilibrated. You may have to run the simulation longer to decide.
   • What is the equilibrium potential energy and kinetic energy?

3. Use the Nose thermostat to set the temperature at kT=1 by adding the NOSE keyword to the input file.
   • Use 20000 time steps and an inverse mass parameter of .01. Try several larger values for the inverse mass (ie, smaller mass).
   • Look at the total energy and note the effect of changing the mass parameter.
   • Look at the extended system energy, and verify that it is conserved.
   • Find the equilibrium potential and kinetic energy, and compare with the values obtained from the constant energy simulation (ie, no thermostat)

Move on to Exercise 2