Virtual Molecular Dynamics Feature Tour

1. Virtual Molecular Dynamics
Feature Tour

2. Virtual Molecular Dynamics Laboratory gives you access to a set of virtual experiments and movies which correspond
to educational materials developed by our research group.
You can open an experiment from any of the existing groups of files, or you can create new groups of files and save
new experiments and movies of your own design.

3. Here is an example of one of many existing groups, Brownian Motion. You can see four types of files :
Simple Molecular Dynamics (SMD) Movie,
Simple Molecular Dynamics Simulation
Universal Molecular Dynamic (UMD) Simulation
Universal Molecular Dynamic Movie.

4. The Meaning of a Model. SMD and UMD are models. Generally speaking, the
purpose of a model is to simplify reality so that reality can be analyzed. For
example, our SMD model contains at most 200 particles in a two-dimensional box. If
a model is only partially successful in predicting behavior, we attempt to modify the
model and improve its assumptions so that its predictions will be more accurate.
This process tends to generate models that are increasingly complex, models that
provide further challenge to scientific investigation. UMD is a model with different
assumptions. SMD and UMD are also simulations. A simulation can be thought of as
putting the model into action. In our case, we program the model into the computer
and begin computing interactions. During simulation, you can change the
parameters such temperature interactively, so, like in a real experiment, the result of
the simulation is not known in advance. The movie is the sequence of screen shots
and parameter values recorded during a simulation. You can watch the movie, but
you cannot change its outcome. Movies are useful for quick demonstration of long
and complex simulations which have taken many hours to be carried out.

5. SMD OVERVIEW: Simple Molecular Dynamics (SMD) is based on the same
simulation algorithms used by research scientists. Our model simulates the
interactions between spherical atoms of noble gases such as helium, neon, argon,
and krypton. SMD allows students to manipulate parameters such as pressure,
volume, temperature, particle number density, and particle mass. Students are also
able to design their own experiments, visualize atoms and their behaviors, and
obtain in-depth, quantitative data which they can graph in many different ways.
VMDL also allows students to view and analyze movies they have created
themselves of previously-saved simulations.