Rose A Gogal, Aaron J Nessler, Andrew C Thiel, Hernan V Bernabe, Rae A Corrigan Grove, Leah M Cousineau, Jacob M Litman, Jacob M Miller, Guowei Qi, Matthew J Speranza, Mallory R Tollefson, Timothy D Fenn, Jacob J Michaelson, Okimasa Okada, Jean-Philip Piquemal, Jay W Ponder, Jana Shen, Richard J H Smith, Wei Yang, Pengyu Ren, Michael J Schnieders
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引用次数: 0
摘要
Force Field X(FFX)是一款开源软件包,用于对基因变体和有机晶体进行原子分辨率建模,它利用了先进的势能函数和实验数据。FFX 目前由九个模块化软件包组成,其新颖的算法包括通过多体扩展进行全局优化、使用可极化的恒pH分子动力学进行酸碱化学反应、自由能差估算、广义柯克伍德隐式溶剂模型等。FFX 的应用主要集中在晶体结构预测管道的使用和开发、根据实验数据集完善生物分子结构,以及估算遗传变异对蛋白质和核酸的热力学影响。并行 Java 和 OpenMM 的结合使用为高性能仿真提供了共享内存、消息传递和图形处理单元并行化。总之,FFX 平台是研究从有机晶体到溶解生物分子系统的计算显微镜。
Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment.
Force Field X (FFX) is an open-source software package for atomic resolution modeling of genetic variants and organic crystals that leverages advanced potential energy functions and experimental data. FFX currently consists of nine modular packages with novel algorithms that include global optimization via a many-body expansion, acid-base chemistry using polarizable constant-pH molecular dynamics, estimation of free energy differences, generalized Kirkwood implicit solvent models, and many more. Applications of FFX focus on the use and development of a crystal structure prediction pipeline, biomolecular structure refinement against experimental datasets, and estimation of the thermodynamic effects of genetic variants on both proteins and nucleic acids. The use of Parallel Java and OpenMM combines to offer shared memory, message passing, and graphics processing unit parallelization for high performance simulations. Overall, the FFX platform serves as a computational microscope to study systems ranging from organic crystals to solvated biomolecular systems.
期刊介绍:
The Journal of Chemical Physics publishes quantitative and rigorous science of long-lasting value in methods and applications of chemical physics. The Journal also publishes brief Communications of significant new findings, Perspectives on the latest advances in the field, and Special Topic issues. The Journal focuses on innovative research in experimental and theoretical areas of chemical physics, including spectroscopy, dynamics, kinetics, statistical mechanics, and quantum mechanics. In addition, topical areas such as polymers, soft matter, materials, surfaces/interfaces, and systems of biological relevance are of increasing importance.
Topical coverage includes:
Theoretical Methods and Algorithms
Advanced Experimental Techniques
Atoms, Molecules, and Clusters
Liquids, Glasses, and Crystals
Surfaces, Interfaces, and Materials
Polymers and Soft Matter
Biological Molecules and Networks.