Home
ASyncRE is a Python package to perform file-based asynchronous parallel replica exchange molecular simulations.
The current implementation is aimed at computer clusters managed by a queuing system and supported by a shared filesystem. The BigJob distributed computing infrastructure is used for job launching and monitoring. Instructions on how to install BigJob on a cluster are available at the following link. While primarily directed at NSF XSEDE clusters, BigJob supports most cluster configurations.
The ASyncRE package includes a core module which performs common tasks such as job staging through BigJob and exchanging of parameters among replicas. Support for arbitrary MD engines and RE schemes are introduced through user-provided modules. Currently, MD engine modules are available for the AMBER and IMPACT MD programs. A similar modular mechanism provides support for arbitrary RE schemes (temperature, Hamiltonian, etc.), including arbitrary multidimensional combinations of these (such as 2D RE temperature/Hamiltonian). The software is currently distributed with modules for multidimensional RE umbrella sampling with AMBER, and BEDAM lambda-RE alchemical binding free energy calculations with the Impact MD engine.
For questions and comments, please join the async-replica-exchange group:
|
| Subscribe to async-replica-exchange |
| Email: |
| Visit this group |