Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, Trieste 34136, Italy.
J Chem Phys. 2020 Sep 21;153(11):114107. doi: 10.1063/5.0020514.
Molecular dynamics simulations require barostats to be performed at a constant pressure. The usual recipe is to employ the Berendsen barostat first, which displays a first-order volume relaxation efficient in equilibration but results in incorrect volume fluctuations, followed by a second-order or a Monte Carlo barostat for production runs. In this paper, we introduce stochastic cell rescaling, a first-order barostat that samples the correct volume fluctuations by including a suitable noise term. The algorithm is shown to report volume fluctuations compatible with the isobaric ensemble and its anisotropic variant is tested on a membrane simulation. Stochastic cell rescaling can be straightforwardly implemented in the existing codes and can be used effectively in both equilibration and production phases.
分子动力学模拟需要在恒定压力下进行 barostat 操作。通常的做法是首先使用 Berendsen 压力控制器,它在平衡时显示出一阶体积弛豫效率,但会导致不正确的体积波动,然后使用二阶或蒙特卡罗压力控制器进行生产运行。在本文中,我们引入了随机细胞缩放,这是一种通过包含合适的噪声项来采样正确体积波动的一阶压力控制器。该算法被证明可以报告与等压系综兼容的体积波动,并且在膜模拟中对其各向异性变体进行了测试。随机细胞缩放可以在现有的代码中直接实现,并可以在平衡和生产阶段有效地使用。