Adapting the semi-explicit assembly solvation model for estimating water-cyclohexane partitioning with the SAMPL5 molecules.
Adapting the semi-explicit assembly solvation model for estimating water-cyclohexane partitioning with the SAMPL5 molecules.
复制标题
适应半明确的组装溶剂化模型，以用Sampl5分子估算水环己烷分配。
DOI：
10.1007/s10822-016-9961-9
复制
发表时间：
2016-11
影响因子：
3.5
通讯作者：
Dill KA
中科院分区：
文献类型：
--
作者：
Brini E;Paranahewage SS;Fennell CJ;Dill KA
我们在这里描述了我们在SAMPL5公共活动“半显式组装”（SEA）中进行的一些测试，SEA是一种计算溶剂化自由能的新方法。我们将SAMPL5的前瞻性测试与后续回顾性计算相结合，以改进SEA现场变体的两个技术方面。首先，SEA使用溶质周围的近似解析面来计算水势。我们改进并简化了该曲面的数学模型。其次，SAMPL5中的一些溶质足够大，需要一种方法来处理与“埋藏原子”（即溶质的内部原子）相互作用的溶剂化水。我们通过埋原子校正改进了SEA。我们还将SEA与热力学积分分子动力学模拟进行了比较，以便整理出力场误差。
We describe here some tests we made in the SAMPL5 communal event of `Semi-Explicit Assembly' (SEA), a recent method for computing solvation free energies. We combined the prospective tests of SAMPL5 with followup retrospective calculations, to improve two technical aspects of the field variant of SEA. First, SEA uses an approximate analytical surface around the solute on which a water potential is computed. We have improved and simplified the mathematical model of that surface. Second, some of the solutes in SAMPL5 were large enough to need a way to treat solvating waters interacting with `buried atoms', i.e. interior atoms of the solute. We improved SEA with a buried-atom correction. We also compare SEA to Thermodynamic Integration molecular dynamics simulations, so that we can sort out force field errors.