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开放力场计划:用于分子建模的开放软件与开放科学

The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling.

作者信息

Wang Lily, Behara Pavan Kumar, Thompson Matthew W, Gokey Trevor, Wang Yuanqing, Wagner Jeffrey R, Cole Daniel J, Gilson Michael K, Shirts Michael R, Mobley David L

机构信息

Open Force Field, Open Molecular Software Foundation, Davis, California 95616, United States.

Center for Neurotherapeutics, University of California, Irvine, California 92697, United States.

出版信息

J Phys Chem B. 2024 Jul 25;128(29):7043-7067. doi: 10.1021/acs.jpcb.4c01558. Epub 2024 Jul 11.

Abstract

Force fields are a key component of physics-based molecular modeling, describing the energies and forces in a molecular system as a function of the positions of the atoms and molecules involved. Here, we provide a review and scientific status report on the work of the Open Force Field (OpenFF) Initiative, which focuses on the science, infrastructure and data required to build the next generation of biomolecular force fields. We introduce the OpenFF Initiative and the related OpenFF Consortium, describe its approach to force field development and software, and discuss accomplishments to date as well as future plans. OpenFF releases both software and data under open and permissive licensing agreements to enable rapid application, validation, extension, and modification of its force fields and software tools. We discuss lessons learned to date in this new approach to force field development. We also highlight ways that other force field researchers can get involved, as well as some recent successes of outside researchers taking advantage of OpenFF tools and data.

摘要

力场是基于物理的分子建模的关键组成部分,它将分子系统中的能量和力描述为所涉及原子和分子位置的函数。在此,我们提供一份关于开放力场(OpenFF)计划工作的综述和科学现状报告,该计划专注于构建下一代生物分子力场所需的科学、基础设施和数据。我们介绍OpenFF计划及相关的OpenFF联盟,描述其力场开发和软件的方法,并讨论迄今取得的成就以及未来计划。OpenFF根据开放且宽松的许可协议发布软件和数据,以实现其力场和软件工具的快速应用、验证、扩展和修改。我们讨论了在这种新的力场开发方法中迄今所吸取的经验教训。我们还强调了其他力场研究人员可以参与的方式,以及外部研究人员利用OpenFF工具和数据取得的一些近期成功案例。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e646/11284797/b106ea62669b/jp4c01558_0001.jpg

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