In these cases exchanges among replicas are implemented using inter-process communication libraries, such as the Message Passing Interface (MPI). Synchronous RE is a suitable algorithm for dedicated High Performance Computing (HPC) clusters where MD threads can efficiently execute in parallel at equal speeds for extended periods of time without failures. In conventional synchronous implementations of RE, parameter exchanges occur simultaneously for all replicas after, for example, the completion of a given number of MD steps. Accelerated conformational sampling is achieved because conformational transitions can occur at the thermodynamic state where they are most likely, rather than only at the thermodynamic state of interest, where they may be rare.īecause RE is inherently a parallel sampling algorithm, it is particularly suited for large high performance computing (HPC) clusters. Hence, each replica travels in conformational space as well as in thermodynamic space. RE methods are based on replicating the system across combinations of thermodynamic and potential energy parameters (in this work primarily alchemical receptor-ligand coupling λ and temperature T), each evolving independently with the exception of occasional exchanges of thermodynamic parameters between replicas. Replica Exchange (RE) algorithms are recognized as among the most powerful enhanced conformational sampling tools available, yielding converged results orders of magnitude faster than conventional approaches. Results produced by biased sampling methods are typically analyzed using post-processing to recover true (unbiased) thermodynamic observables. An important class of methods are based on the imposition of thermodynamic or mechanical biasing forces which can speed up, often by many orders of magnitude, conformational interconversions otherwise too rare to be observed in traditional simulations. Enhanced conformational sampling algorithms have been developed to accelerate the modeling of these processes so that they can be studied in reasonable time frames. Many physiochemical processes, such as phase transitions and the folding and binding of proteins, occur on time scales difficult to access even with the fastest supercomputers available. They show the ability of ASyncRE to utilize large grids of desktop computers running the Windows, MacOS, and/or Linux operating systems as well as collections of high performance heterogeneous hardware devices.
BOINC RENDER FARM SOFTWARE
Applications of the software for the modeling of association equilibria of supramolecular and macromolecular complexes on BOINC campus computational grids and on the CPU/MIC heterogeneous hardware of the XSEDE Stampede supercomputer are illustrated. ASyncRE is written in Python following a modular design conducive to extensions to various replica exchange schemes and molecular dynamics engines. It allows molecular dynamics threads to progress at different rates and enables parameter exchanges among arbitrary sets of replicas independently from other replicas. The asynchronous replica exchange algorithm on which the software is based avoids centralized synchronization steps and the need for direct communication between remote processes. Here we describe the architecture of a software (named ASyncRE) for performing asynchronous replica exchange molecular simulations on volunteered computing grids and heterogeneous high performance clusters. Inter-process communication and coordination requirements have historically discouraged the deployment of replica exchange on distributed and heterogeneous resources. Parallel replica exchange sampling is an extended ensemble technique often used to accelerate the exploration of the conformational ensemble of atomistic molecular simulations of chemical systems.
0 kommentar(er)
