论文标题
在恒压下从长时间分子动力学模拟的扩散系数的系统误差
Systematic errors in diffusion coefficients from long-time molecular dynamics simulations at constant pressure
论文作者
论文摘要
在周期性边界条件下的分子动力学模拟中，粒子位置通常包裹在参考框中。对于使用爱因斯坦关系的扩散系数计算，需要解开粒子位置。在这里，我们表明一种广泛使用的启发式拆箱方案不适用于在恒定压力下长时间的模拟。对于盒子体积波动的不当，很长一段时间都会导致非物理轨迹，进而构成严重夸大的扩散系数。我们提出了解决此问题的替代拆开计划。在每个时间步骤中，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。在这里和同伴论文中[J。化学物理。 XXX，Yyyyy（2020）]，我们将新的未包装方案应用于广泛的分子动力学和布朗动力学模拟数据。我们为从业人员提供了一个公式，以评估是否及其较早的结果可能受到广泛使用的启发式拆开计划的影响。
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 a companion paper [J. Chem. Phys. XXX, YYYYY (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.
