Replica exchange with solute scaling: a more efficient version of replica exchange with solute tempering (REST2).
Replica exchange with solute scaling: a more efficient version of replica exchange with solute tempering (REST2).
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DOI：
10.1021/jp204407d
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发表时间：
2011-08-04
影响因子：
3.3
通讯作者：
Berne, B. J.
中科院分区：
文献类型：
--
作者：
Wang, Lingle;Friesner, Richard A.;Berne, B. J.
副本交换溶质回火(REST)中哈密顿标度的微小变化可以大大提高其采样效率，特别是对于溶质构象发生大范围变化的蛋白质水溶液的采样。与原始REST(REST1)一样，新版本(我们称为REST2)也绕过了标准温度副本交换方法(TREM)的系统大小扩展不佳的问题，减少了必须在TREM中使用的副本(并行进程)数量。通过使每个复制品的哈密顿函数变形，使得复制品构型交换的接受概率不依赖于系统中显式水分子的数量，来实现这种简化。为了验证概念，比较了REST2与TREM以及REST1在水中折叠三叶笼和β-发夹的效果。比较证明，REST2大大减少了常规副本交换所需的CPU数量，大大提高了采样效率。这种方法减少了计算热力学平均值和蛋白质在显性水中从头计算折叠所需的CPU时间。
A small change in the Hamiltonian scaling in replica exchange with solute Tempering (REST) is found to improve its sampling efficiency greatly especially for the sampling of aqueous protein solutions in which there are large scale solute conformation changes. Like the original REST (REST1), the new version (which we call REST2) also bypasses the poor scaling with system size of the standard temperature replica exchange method (TREM), reducing the number of replicas (parallel processes) from what must be used in TREM. 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, REST2 is compared with TREM and with REST1 for the folding of the trpcage and β-hairpin in water. The comparisons confirm that REST2 greatly reduces the number of CPUs required by regular replica exchange and greatly increases the sampling efficiency over REST1. This method reduces the CPU time required for calculating thermodynamic averages and for the ab initio folding of proteins in explicit water.
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影响因子：
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作者：
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