Höllmer Philipp, Maggs A C, Krauth Werner
Physikalisches Institut and Bethe Center for Theoretical Physics, University of Bonn, Nussallee 12, 53115, Bonn, Germany.
CNRS UMR7083, ESPCI Paris, Université PSL, 10 Rue Vauquelin, 75005, Paris, France.
Sci Rep. 2024 Jul 16;14(1):16449. doi: 10.1038/s41598-024-66172-0.
In a world made of atoms, computer simulations of molecular systems such as proteins in water play an enormous role in science. Software packages for molecular simulation have been developed for decades. They all discretize Hamilton's equations of motion and treat long-range potentials through cutoffs or discretization of reciprocal space. This introduces severe approximations and artifacts that must be controlled algorithmically. Here, we bring to fruition a paradigm for molecular simulation that relies on modern concepts in statistics to explore the thermodynamic equilibrium with an exact and efficient non-reversible Markov process. It is free of all discretizations, approximations, and cutoffs. We explicitly demonstrate that this approach reaches a break-even point with traditional molecular simulation performed at high precision, but without any of its approximations. We stress the potential of our paradigm for crucial applications in biophysics and other fields, and as a practical approach to molecular simulation. We set out a strategy to reach our goal of rigorous molecular simulation.
在一个由原子构成的世界里，诸如水中蛋白质等分子系统的计算机模拟在科学中发挥着巨大作用。用于分子模拟的软件包已经开发了数十年。它们都对哈密顿运动方程进行离散化处理，并通过截断或倒易空间离散化来处理长程势。这引入了必须通过算法控制的严重近似和伪影。在此，我们实现了一种分子模拟范式，该范式依赖于统计学中的现代概念，通过精确且高效的不可逆马尔可夫过程来探索热力学平衡。它没有任何离散化、近似和截断。我们明确证明，这种方法与高精度执行的传统分子模拟达到了收支平衡点，但没有其任何近似。我们强调我们的范式在生物物理学和其他领域关键应用中的潜力，以及作为分子模拟的一种实用方法的潜力。我们制定了实现严格分子模拟目标的策略。
