Virtual Molecular Dynamics Feature Tour

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Virtual Molecular Dynamics Feature Tour
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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.
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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.
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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.
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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.
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