If you think you have a straightforward question, please check
the online documentation
first to see if it answers your questions. In particular, check
the FAQ.
DynamO is a research project which has been open-sourced to help
push forward both event-driven algorithms and discrete-potential
models. The best way to recieve support is to contact and
collaborate with researchers/developers familiar with DynamO.
Contacting the Developers
You can contact the developers of DynamO by emailing the following
address:
If it turns out that you've discovered a bug in DynamO, you will be
encouraged to post a bug report on the Github issue tracker so you
can track when the bug is fixed.
Reporting Bugs
If you think you've found a bug, please report it using the GitHub
Issue tracker link below. The bug tracker allows others to see how
your problem might be resolved and it also allows you to track the
progress in dealing with any reported issues.
Please note, you will need a (free) GitHub account.
Alternatives
If all else fails, there are some alternative event-driven packages
(and groups) available and they are listed here:
-
PackLSD
(or an older
version):
This is powerful code aimed at generating
densely packed hard particle (ellipsoidal) configurations. DynamO
uses the same techniques for compression but it is currently
limited to spheres or shapes composed of multiple spheres. The
PackLSD code is simpler as it is targeted only to the task of
generating hard particle packings, yet more advanced in that it
handles ellipsoids. It also contains tools for analysing the
packed configuration.
-
iFold: This is
an event driven simulator for protein simulations presented by the
Dokholyan group. It doesn't appear that the simulator is
publically available.
-
SPEADMD : This is a
collection of event driven potentials and Thermodynamic
Perturbation Theory (TPT) which can be used to accurately estimate
the thermophysical properties of compounds. The results are
extremely impressive and details on the potential parameters are
reported in publications. The simulation code does not appear to
be publically available but simulations can be requested through a
web interface.
-
Cellular Dynamic
Simulator:
An impressive package designed to simulate
biological processes. Includes support for triangle meshes,
brownian dynamics, and also has its own 3D visualizer.
-
MDdMD:
A
web interface to a EDMD code for studying conformational
transitions with coarse-grained discrete models. Appears to be
closed source but openly accessible.
-
Event-Chain
Algorithm:
A remarkable event-driven algorithm
capable of evolving discrete and continuous potential
configurations. Not molecular dynamics but a great example of
advanced algorithmic ideas from the event driven particles
field.
-
Hardballs:
This appears to be the start of 2D EDMD simulation code.
-
etomica: Java code for
simulating hard-spheres, square-wells, and a wide range of other
models.
Page last modified: Thursday 29th July 2021
