Distributed Replica (DR) sampling is a generalized ensemble simulation algorithm wherein
sampling occurs amongst a collection of ensembles that are distributed along a predetermined reaction
coordinate. During DR, sampling is generated by multiple replicas that each undergo a random walk
along this reaction coordinate, weakly coupled by the Distributed Replica potential energy function
(DRPE). For a more complete description of DR sampling, see T. Rodinger, P.L. Howell, and R. Pomès,
"Distributed Replica Sampling" J. Chem. Theory Comput., 2:725 (2006).
The Distributed Replica Sampling Software Suite (DRSSS) is an implementation of DR
sampling. The purpose of this document is the description of the Distributed Replica Sampling
Software Suite.
DRSSS completely abstracts the implementation of the molecular dynamic simulation (MD) or
Monte Carlo simulation (MC) from the DR sampling and the DRPE. Users may therefore combine the
DRSSS software with any simulations package (for example: GROMACS, CHARMM, or NAMD).
While this level of abstraction is useful, it means that the end user is responsible for a significant level
of scripting to control the actual MD/MC simulation and to then provide the relevant information in
formatted files that will be transmitted back to the server by the DRSSS.