Molecular Dynamics Lab Exercises

The purpose of these exercises is to introduce you to elementary simulations using Molecular Dynamics.

We are using a program called CLAMPS (CLAssical Many Particle Simulator)

The main CLAMPS page has information about the methods and the input file. You can also look at the DataSpork main page for information on the DataSpork analysis program.

To get started, type source /cms/ceperley.cshrc. This will set some environment variables, and make a clamps directory for you to work in. To run clamps, just type clamps. To run DataSpork, just type dataspork, and use the File/Open Datasets menu to open datasets with the appropriate data reader.

  1. Getting Started. Basics of statistical data analysis. Introduction to DataSpork software.
  2. Exercise 1. Introduction to MD. Constant Temperature with a Nose Thermostat.
  3. Exercise 2. Introduction to Correlation Functions.
When you finish, you can look at the solutions.
  1. Getting Started Solutions
  2. Exercise 1 Solutions
  3. Exercise 2 Solutions

The output can be viewed and analyzed with the DataSpork program. The data can also be viewed with gnuplot

Back to David Ceperley's Introduction to Computer Simulation of Atomic-Scale Systems