Video Gallery
In this section, a range of sample videos of DynamO simulations are
presented to highlight what is currently possible with the code and
to give an idea of its speed. The videos below are all running in
real time or have been slowed down to allow a clearer animation. The
majority of the videos have been produced using the Coil
visualisation software, which is included as a part of DynamO.
Full List of Features
Key Features
DynamO has the following features:

Smooth or rough hard spheres, square
wells, soft cores, stepped potentials and all
the other simple EDMD potentials are fully supported. Some
complex interactions, such as hard lines and part of the
PRIME model for protiens, are also supported.

Millions of particles for billions of events. Using
500 bytes per particle and running at around 75k events per
second, DynamO is one of the most efficient and fastest
eventdriven simulators available.
 Transport Properties: DynamO automatically collects
information on all of the transport coefficients for the simulated
fluid, including the thermal conductivity, viscosity, self and
mutual diffusion, and thermal diffusion coefficients. These are
collected using the Einstein form of the GreenKubo expressions.

NonEquilibrium Molecular Dynamics (NEMD): DynamO has
thermostats, thermalised walls, and LeesEdwards boundary
conditions for shearing systems, allowing the study of a wide
range of NonEquilibrium data.

Compression dynamics: Need to study high density systems?
DynamO can compress most of its model systems using isotropic
compaction, allowing you to start from a low density where it is
easier to place the particles.

Polydispersity: All interactions are
generalised to fully polydisperse particles.

Stable handling of overlapped states: Thanks to a careful
implementation of the eventdetection routines in DynamO, it can
safely recover from invalid states caused by overlapped cores in
most cases. This makes DynamO the most stable eventdriven
particle dynamics code, and this feature is essential
in granular systems.
Granular Systems/Complex Boundaries
DynamO contains all the latest EDMD algorithms for dissipative
systems:

Event driven dynamics with gravity: All interactions work
in the presence of gravity, allowing event driven simulations of
macroscopic systems.

Sleeping particles: In systems where particles
come to a rest, the sleeping particles algorithm can remove the cost
of simulating the particles completely.

Triangle or sphere meshes: Arbitrary complex
boundaries can be implemented using triangle meshes imported from
CAD drawings.

Stepped potentials: Arbitrary stepped potentials
may be simulated to approximate any soft potential.
Polymeric Systems/Accelerated Dynamics
Dynamo has extremely advanced algorithms for accelerated dynamics:

Parallel tempering/Replica exchange: Run multiple
simulations in parallel and use this Monte Carlo technique to
enhance the sampling of phase space when it is energetically
difficult. This is essential in protein/polymerfolding
simulations.

Histogram reweighting: Combine the results from replica
exchange simulations and extrapolate to temperatures which were
not simulated, maximising the information extracted.

Multicanonical simulations: Used either in conjunction with
or as a replacement for replica exchange techniques,
multicanonical simulations greatly enhance the sampling of phase
space, helping find the true native states of the polymer.
Page last modified: Thursday 29th May 2014