Programming Credits
-
Marcus Bannerman: DynamO was originally developed
during Marcus' PhD, under the supervision of Dr Leo Lue and was
funded through a EPSRC doctoral training award. From 2009 till
2011, this work continued during his Post-Doc at the University of
Erlangen-Nuremberg in the research group of Prof. Thorsten
Poeschel. Now Marcus is a lecturer at Aberdeen University and
continues to orientate his research around DynamO and event driven
simulators.
-
Leo Lue: Provided a complete event driven code, histogram
reweighting scripts, and more which were used as reference
implementations while DynamO was developed. Leo provides a great
amount of theoretical/technical support and implemented the MJ
model for protein interactions.
- Gil Rutter: Gil implemented the PRIME protein potential,
which is the first complex multi-site potential in DynamO. This
required significant development and determination of the
free/unpublished model parameters. Gil continues to work on
developing this model.
-
Robert Sargant: Robert began the implementation of
asymmetric potentials with rotational degrees of freedom. He
implemented the dynamics of lines and the root finder of Frenkel
and Maguire among other improvements. Robert was funded by the
EPSRC under a DTA award.
Libraries and Source Code Used
-
XML parsing uses RapidXML.
-
XML writing uses a small class provided by Obolutus.
-
Gtkmm, Cairo, FFMPEG
and the boost libraries are
some excellent open source libraries utilised within the code.
-
The build system used is the CMake system.
-
Bosco ho provided
the reference
script from which the RMSD calculations of polymer structures
script is based.
-
MinMax Heaps are based on an implementation provided
by T. Wease.
-
A small PNG library is used for saving snapshots and was provided
by Severin Strobl.
-
Thank you to Michael R Sweet for creating fldiff, a program which
makes it so easy to compare good and bad EDMD trajectories and has
saved hours of debugging in the scheduler code. This has now been
superceeded by the meld program.
-
Cédric Laugerotte's website (now offline) was a great help for determining
tesselations of spheres.
Page last modified: Sunday 9th June 2024
