期刊
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
卷 13, 期 9, 页码 4003-4011出版社
AMER CHEMICAL SOC
DOI: 10.1021/acs.jctc.7b00480
关键词
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资金
- Acellera Ltd
- MINECO [BIO2014-53095-P]
- FEDER
HTMD is a programmable scientific platform intended to facilitate simulation-based research in molecular systems. This paper presents the functionalities of HTMD for the preparation of a molecular dynamics simulation starting from PDB structures, building the system using well-known force fields, and applying standardized protocols for running the simulations. We demonstrate the framework's flexibility for high-throughput molecular simulations by applying a preparation, building, and simulation protocol with multiple force-fields on all of the seven hundred eukaryotic membrane proteins resolved to-date from the orientation of proteins in membranes (OPM) database. All of the systems are available on www.playmolecule.org.
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