Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.
J Chem Phys. 2020 Jul 14;153(2):021101. doi: 10.1063/5.0008316.
In molecular dynamics simulations under periodic boundary conditions, particle positions are typically wrapped into a reference box. For diffusion coefficient calculations using the Einstein relation, the particle positions need to be unwrapped. Here, we show that a widely used heuristic unwrapping scheme is not suitable for long simulations at constant pressure. Improper accounting for box-volume fluctuations creates, at long times, unphysical trajectories and, in turn, grossly exaggerated diffusion coefficients. We propose an alternative unwrapping scheme that resolves this issue. At each time step, we add the minimal displacement vector according to periodic boundary conditions for the instantaneous box geometry. Here and in another paper [J. T. Bullerjahn, S. von Bülow, and G. Hummer, J. Chem. Phys. 153, 024116 (2020)], we apply the new unwrapping scheme to extensive molecular dynamics and Brownian dynamics simulation data. We provide practitioners with a formula to assess if and by how much earlier results might have been affected by the widely used heuristic unwrapping scheme.
在周期性边界条件下的分子动力学模拟中，粒子位置通常被包裹在参考盒中。对于使用爱因斯坦关系计算扩散系数，需要对粒子位置进行展开。在这里，我们表明，一种广泛使用的启发式展开方案不适用于恒压下的长时间模拟。不正确地考虑盒体积波动会在长时间内产生非物理轨迹，并进而极大地夸大扩散系数。我们提出了一种替代的展开方案来解决这个问题。在每个时间步，我们根据瞬时盒几何形状的周期性边界条件添加最小位移矢量。在本文和另一篇论文[J.T.布勒扬、S.冯·布洛伊和 G.哈默尔，J.化学物理 153,024116（2020）]中，我们将新的展开方案应用于广泛的分子动力学和布朗动力学模拟数据。我们为从业者提供了一个公式，以评估先前的结果是否以及受到了广泛使用的启发式展开方案的影响，以及影响的程度。
