Reif Maria M, Oostenbrink Chris
Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria.
Theor Chem Acc. 2015;134(2):2. doi: 10.1007/s00214-014-1600-8. Epub 2015 Jan 10.
Despite considerable advances in computing power, atomistic simulations under nonperiodic boundary conditions, with Coulombic electrostatic interactions and in systems large enough to reduce finite-size associated errors in thermodynamic quantities to within the thermal energy, are still not affordable. As a result, periodic boundary conditions, systems of microscopic size and effective electrostatic interaction functions are frequently resorted to. Ensuing artifacts in thermodynamic quantities are nowadays routinely corrected a posteriori, but the underlying configurational sampling still descends from spurious forces. The present study addresses this problem through the introduction of on-the-fly corrections to the physical forces during an atomistic molecular dynamics simulation. Two different approaches are suggested, where the force corrections are derived from special potential energy terms. In the first approach, the solvent-generated electrostatic potential sampled at a given atom site is restrained to a target value involving corrections for electrostatic artifacts. In the second approach, the long-range regime of the solvent polarization around a given atom site is restrained to the Born polarization, i.e., the solvent polarization corresponding to the ideal situation of a macroscopic system under nonperiodic boundary conditions and governed by Coulombic electrostatic interactions. The restraints are applied to the explicit-water simulation of a hydrated sodium ion, and the effect of the restraints on the structural and energetic properties of the solvent is illustrated. Furthermore, by means of the calculation of the charging free energy of a hydrated sodium ion, it is shown how the electrostatic potential restraint translates into the on-the-fly consideration of the corresponding free-energy correction terms. It is discussed how the restraints can be generalized to situations involving several solute particles. Although the present study considers a very simple system only, it is an important step toward the on-the-fly elimination of finite-size and approximate-electrostatic artifacts during atomistic molecular dynamics simulations.
尽管计算能力有了显著进步，但在非周期性边界条件下，考虑库仑静电相互作用且系统规模大到足以将热力学量中与有限尺寸相关的误差降低到热能范围内的原子模拟，仍然成本高昂。因此，人们经常采用周期性边界条件、微观尺寸的系统和有效的静电相互作用函数。如今，热力学量中随之产生的伪像通常会在事后进行校正，但潜在的构型采样仍然源于虚假力。本研究通过在原子分子动力学模拟过程中对物理力引入实时校正来解决这个问题。提出了两种不同的方法，其中力的校正源自特殊的势能项。在第一种方法中，将在给定原子位点采样的溶剂产生的静电势限制在一个涉及静电伪像校正的目标值。在第二种方法中，将给定原子位点周围溶剂极化的长程区域限制在玻恩极化，即对应于非周期性边界条件下宏观系统的理想情况且由库仑静电相互作用支配的溶剂极化。这些限制应用于水合钠离子的显式水模拟，并说明了这些限制对溶剂的结构和能量性质的影响。此外，通过计算水合钠离子的充电自由能，展示了静电势限制如何转化为对相应自由能校正项的实时考虑。还讨论了如何将这些限制推广到涉及多个溶质粒子的情况。尽管本研究仅考虑了一个非常简单的系统，但这是朝着在原子分子动力学模拟过程中实时消除有限尺寸和近似静电伪像迈出的重要一步。
