Path Integral Coarse-Graining Replica Exchange Method for Enhanced Sampling

被引:12
|
作者
Peng, Yuxing [1 ,2 ]
Cao, Zhen [1 ,2 ]
Zhou, Ruhong [3 ]
Voth, Gregory A. [1 ,2 ]
机构
[1] Univ Chicago, Dept Chem, James Franck Inst, Chicago, IL 60637 USA
[2] Univ Chicago, Computat Inst, Chicago, IL 60637 USA
[3] IBM Corp, Thomas J Watson Res Ctr, Computat Biol Ctr, Yorktown Hts, NY 10598 USA
基金
美国国家科学基金会;
关键词
MOLECULAR-DYNAMICS SIMULATIONS; HISTOGRAM ANALYSIS METHOD; FREE-ENERGY CALCULATIONS; ALANINE DIPEPTIDE; EXPLICIT WATER; MEAN FORCE; GAS-PHASE; PROTEIN; OPTIMIZATION; CONVERGENCE;
D O I
10.1021/ct500447r
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
An enhanced conformational space sampling method is developed that utilizes replica exchange molecular dynamics between a set of imaginary time Feynman path integral replicas, each having an increasing degree of contraction (or coarse-graining) of the quasi-particle or polymer beads in the evaluation of the isomorphic ring-polymer potential energy terms. However, there is no contraction of beads in the effectively harmonic kinetic energy terms. The final replica in this procedure is the fully contracted one in which the potential energy is evaluated only at the centroid of the beadsand hence it is the classical distribution in the centroid variablewhile the initial replica has the full degree (or even a heightened degree, if desired) of quantum delocalization and tunneling in the physical potential by the polymer necklace beads. The exchange between the different ring-polymer ensembles is governed by the Metropolis criteria to guarantee detailed balance. The method is applied successfully to several model systems, ranging from one-dimensional prototype rough energy landscape models having analytical solutions to the more realistic alanine dipeptide. A detailed comparison with the classical temperature-based replica exchange method shows an improved efficiency of this new method in the classical conformational space sampling due to coupling with the fictitious path integral (quantum) replicas.
引用
收藏
页码:3634 / 3640
页数:7
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