DISCRETE is a package devised to simulate the dynamics of proteins using the Discrete Molecular Dynamics (DMD) method. The difference with respect to a standard molecular dynamics simulation is that the particles are considered to move with constant velocity until a collision occurs. Upon each collision there is a transfer of linear momentum between the colliding particles, where total momentum and energy are conserved. As the particles move in ballistic regime, the motion equations do not need to be integrated. This leads to saving a drastic amount of computing time. In DMD the interaction potentials are stepwise potentials, and the events (collisions) occur when the distance between two particles corresponds to a step in its interaction potential. DMD is an event-driven method, so the timestep is not predefined like in a standard molecular dynamics simulation, but it is the time between consecutive collisions. The frequency of the collisions in the system increases linearly with the number of particles, and with the number of steps in the interaction potential. Some examples of its usage are described on use case scenarios.
How to use DISCRETE
If you have never used DISCRETE we recommend that you start with the Quick Start guide.
If you are interested in running DISCRETE on supercomputers or clusters, HPC usage will help you to efficiently utilize such resources.
HPC usage will be valuable to IT personnel and administrators - there you can find information about the installation and setup of DISCRETE on powerful supercomputers and clusters.
Software developers may be interested in the Performance section where they can find information on debugging, profiling, analyzing and optimizing the source code. Description of algorithms for high-scalability is also provided in the Performance section.
DISCRETE is also the engine behind the Maxwell-Demon DMD simulator developed at IRB.
ScalaLife is providing also cloud images for several stacks.
Please acknowledge the ScalaLife project and Discrete in your publications following the acknowledgement policy.