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.
- 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.
- 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?
- 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