Replica exchange with solute tempering: A method for sampling biological systems in explicit water
Replica exchange with solute tempering: A method for sampling biological systems in explicit water
复制标题
DOI：
10.1073/pnas.0506346102
复制
发表时间：
2005-09-27
影响因子：
11.1
通讯作者：
Berne, BJ
中科院分区：
文献类型：
--
作者：
Liu, P;Kim, B;Berne, BJ
本文提出了一种新颖的用于蛋白质水溶液高效采样的溶质回火副本交换（REST）方法。该方法绕过了标准副本交换的系统规模的可伸缩性差，从而减少了必须使用的副本（并行进程）的数量。这种减少是通过变形的哈密尔顿函数为每个副本在这样一种方式，副本配置的交换的接受概率不依赖于系统中的显式水分子的数量。为了验证概念，REST与水中丙氨酸二肽分子的标准复制交换进行了比较。比较证实，REST大大减少了常规副本交换所需的CPU数量，并提高了采样效率。这种方法减少了计算热力学平均值和在显式水中蛋白质从头折叠所需的CPU时间。
An innovative replica exchange (parallel tempering) method called replica exchange with solute tempering (REST) for the efficient sampling of aqueous protein solutions is presented here. The method bypasses the poor scaling with system size of standard replica exchange and thus reduces the number of replicas (parallel processes) that must be used. This reduction is accomplished by deforming the Hamiltonian function for each replica in such a way that the acceptance probability for the exchange of replica configurations does not depend on the number of explicit water molecules in the system. For proof of concept, REST is compared with standard replica exchange for an alanine dipeptide molecule in water. The comparisons confirm that REST greatly reduces the number of CPUs required by regular replica exchange and increases the sampling efficiency. This method reduces the CPU time required for calculating thermodynamic averages and for the ab initio folding of proteins in explicit water.