期刊
MOLECULAR PHYSICS
卷 111, 期 22-23, 页码 3345-3362出版社
TAYLOR & FRANCIS LTD
DOI: 10.1080/00268976.2013.813594
关键词
molecular dynamics simulation; collective variable; free-energy calculation; adaptive bias; sampling
资金
- NSF [CHE-1212416]
- NSF-XSEDE [TG-MCA93S020]
- GENCI-CINES [2012-076198]
- Division Of Chemistry
- Direct For Mathematical & Physical Scien [1212416] Funding Source: National Science Foundation
A software framework is introduced that facilitates the application of biasing algorithms to collective variables of the type commonly employed to drive massively parallel molecular dynamics (MD) simulations. The modular framework that is presented enables one to combine existing collective variables into new ones, and combine any chosen collective variable with available biasing methods. The latter include the classic time-dependent biases referred to as steered MD and targeted MD, the temperature-accelerated MD algorithm, as well as the adaptive free-energy biases called metadynamics and adaptive biasing force. The present modular software is extensible, and portable between commonly used MD simulation engines.
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