Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA.
Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA.
J Chem Phys. 2018 Jan 28;148(4):044104. doi: 10.1063/1.5008853.
Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods and that facilitates implementation of new techniques as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques-including adaptive biasing force, string methods, and forward flux sampling-that extract meaningful free energy and transition path data from all-atom and coarse-grained simulations. A noteworthy feature of SSAGES is a user-friendly framework that facilitates further development and implementation of new methods and collective variables. In this work, the use of SSAGES is illustrated in the context of simple representative applications involving distinct methods and different collective variables that are available in the current release of the suite. The code may be found at: https://github.com/MICCoM/SSAGES-public.
分子模拟已成为现代研究的重要工具，但要从模拟中获得正确的结果并得出可靠的结论，需要对所考虑的系统进行充分的采样。为此，文献中存在各种可以大大提高采样效果的方法，并且越来越复杂、有效的算法也在迅速发展。然而，这些技术的实现对专家和非专家来说都是具有挑战性的。显然需要一种软件，它可以快速、可靠、方便地访问广泛的高级采样方法，并促进新技术的实施，因为这些技术会不断涌现。在这里，我们介绍了 SSAGES，这是一个可公开获取的用于高级通用模拟的软件套件，旨在与多个广泛使用的分子动力学模拟包进行接口。SSAGES 允许轻松应用各种增强采样技术，包括自适应偏置力、字符串方法和前向通量采样，从而从全原子和粗粒模拟中提取有意义的自由能和跃迁路径数据。SSAGES 的一个显著特点是用户友好的框架，它促进了新方法和集体变量的进一步开发和实现。在这项工作中，SSAGES 的使用在涉及不同方法和不同集体变量的简单代表性应用中进行了说明，这些方法和集体变量在套件的当前版本中都有提供。该代码可以在以下网址找到：https://github.com/MICCoM/SSAGES-public。
