Replica exchange with solute tempering: Efficiency in large scale systems
Replica exchange with solute tempering: Efficiency in large scale systems
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DOI：
10.1021/jp068826w
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发表时间：
2007-05-17
影响因子：
3.3
通讯作者：
Berne, B. J.
中科院分区：
文献类型：
--
作者：
Huang, Xuhui;Hagen, Morten;Berne, B. J.
我们将最近开发的溶质回火复制交换(REST)应用于三个大型溶剂化多肽系统：α-螺旋、β-发夹和TrpCage，这些多肽被定义为“中心基团”。我们发现我们最初的REST实现并不总是比副本交换方法(REM)更有效。具体地说，我们发现结构能差异很大的折叠构象(F)和展开构象(U)之间的交换由于在副本交换接受概率中不出现水自作用能而大大减少。然而，REST有望在一大类两种状态之间的能量差距不大的系统中仍然有用，例如弱结合的蛋白质-配体复合体。或者，可以将水分子的壳层结合到中心基团中，如原始论文中所讨论的那样。
We apply the recently developed replica exchange with solute tempering (REST) to three large solvated peptide systems: an alpha-helix, a beta-hairpin, and a TrpCage, with these peptides defined as the "central group". We find that our original implementation of REST is not always more efficient than the replica exchange method (REM). Specifically, we find that exchanges between folded (F) and unfolded (U) conformations with vastly different structural energies are greatly reduced by the nonappearance of the water self-interaction energy in the replica exchange acceptance probabilities. REST, however, is expected to remain useful for a large class of systems for which the energy gap between the two states is not large, such as weakly bound protein-ligand complexes. Alternatively, a shell of water molecules can be incorporated into the central group, as discussed in the original paper.