Kamberaj Hiqmet, van der Vaart Arjan
Center for Biological Physics and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA.
J Chem Phys. 2007 Dec 21;127(23):234102. doi: 10.1063/1.2806930.
A multiple scaling replica exchange method for the efficient conformational sampling of biomolecular systems in explicit solvent is presented. The method is a combination of the replica exchange with solute tempering (REST) technique and a Tsallis biasing potential. The Tsallis biasing increases the sampling efficiency, while the REST minimizes the number of replicas needed. Unbiased statistics can be obtained by reweighting of the data using a weighted histogram analysis technique. The method is illustrated by its application to a ten residue peptide in explicit water.
提出了一种用于在显式溶剂中对生物分子系统进行高效构象采样的多重缩放副本交换方法。该方法是溶质回火副本交换（REST）技术与Tsallis偏置势的结合。Tsallis偏置提高了采样效率，而REST则使所需的副本数量最小化。通过使用加权直方图分析技术对数据进行重新加权，可以获得无偏统计量。通过将该方法应用于在纯水中的一个十肽来说明该方法。
