Linear Basis Function Approach to Efficient Alchemical Free Energy Calculations. 2. Inserting and Deleting Particles with Coulombic Interactions
Linear Basis Function Approach to Efficient Alchemical Free Energy Calculations. 2. Inserting and Deleting Particles with Coulombic Interactions
复制标题
DOI：
10.1021/ct501047e
复制
发表时间：
2015-06-01
影响因子：
5.5
通讯作者：
Shirts, Michael R.
中科院分区：
文献类型：
--
作者：
Naden, Levi N.;Shirts, Michael R.
我们扩展了我们以前的线性基函数的炼金术自由能计算方法的插入和删除的带电粒子在稠密的流体。我们计算一个接近最佳的统计路径引入库仑相互作用到各种分子在溶液中，并发现，这种接近最佳的路径只是稍微更有效地比简单的线性耦合的静电在所有情况下，排斥的核心已经存在。我们还探讨了非键合力耦合到炼金术转换的环境中的顺序。我们测试两套Lennard-Jones基函数，一个周钱德勒安德森（WCA）和12-6分解的排斥力和吸引力打开顺序沿着与电荷的变化，以确定一个统计优化的顺序，力应该耦合。WCA分解具有较低的统计不确定性，因为耦合有吸引力的r（-6）基函数贡献不可忽略的统计误差。在所有的情况下，电荷应该在排斥核完全耦合之后才耦合，并且WCA吸引部分可以在任何阶段耦合而不显著改变效率。带电粒子的两个基函数方法的统计不确定性几乎与用于去耦静电的软核方法相同，尽管用于采样的相关十分之一对于软核静电方法通常比基函数方法更长。基函数的方法，用于引入或删除分子或官能团，因此代表了一个有用的替代软核的方法与一些亲爱的计算优势。
We extend our previous linear basis function approach for alchemical free energy calculations to the insertion and deletion of charged particles in dense fluids. We compute A near optimal statistical path to introduce Coulombic interactions into various molecules in solution and find that this near optimal path is only marginally more efficient than simple linear coupling of electrostatics in all cases where a repulsive core is already present. We also explore the order in which nonbonded forces are coupled to the environment in alchemical transformations. We test two sets of Lennard-Jones basis functions, a Weeks Chandler Andersen (WCA) and a 12-6 decomposition of the repulsive and attractive forces turned on in sequence along With changes in charge, to determine a statistically optimized order in which forces should be coupled. The WCA decomposition has lower statistical uncertainty as coupling the attractive r(-6) basis function contributes non-negligible statistical error. In all cases, the charge should be coupled only after the repulsive core is fully coupled, and the WCA attractive portion Can be coupled at any stage without significantly changing the efficiency. The statistical uncertainty of two of the basis function approaches with charged particles is nearly identical to the soft core approach for decoupling electrostatics, though the correlation tithes for sampling are often longer for a soft core electrostatics approach than the basis function approach. The basis function approach for introducing or removing molecules or functional groups thus represents a useful alternative to the soft core approach with a number of dear computational advantages.