Exploiting molecular dynamics in Nested Sampling simulations of small peptides
Exploiting molecular dynamics in Nested Sampling simulations of small peptides
复制标题
DOI：
10.1016/j.cpc.2015.12.005
复制
发表时间：
2016-04-01
影响因子：
6.3
通讯作者：
Csanyi, Gabor
中科院分区：
文献类型：
--
作者：
Burkoff, Nikolas S.;Baldock, Robert J. N.;Csanyi, Gabor
嵌套抽样（NS）是一种参数空间抽样算法，可用于原子系统平衡热力学的抽样。NS先前已用于探索粗粒度蛋白质模型的势能面，并且在计算Lennard-Jones簇的热容曲线时明显优于并行回火。原始NS算法使用蒙特卡罗（MC）移动；然而，最近引入了一种变体，Galilean NS，它允许将NS纳入分子动力学框架，因此NS可以用于缺乏有效规定MC移动的系统。在这项工作中，我们证明了伽利略NS对原子系统的适用性。我们使用Amber分子动力学包实现了Galilean NS，并通过在真空和隐式溶剂中取样丙氨酸二肽来证明其可行性。与以往的研究不同，我们提出了丙氨酸二肽的热容曲线，其计算为采样算法提供了严格的检验。我们还将计算结果与复制交换分子动力学（REMD）计算结果进行了比较，发现了很好的一致性。我们展示了计算的努力需要准确的热容估计小肽。我们还计算了一定温度下的丙氨酸二肽Ramachandran自由能面，并将最新琥珀力场的结果与以往的理论和实验结果进行了比较。(C) 2016年作者。Elsevier B.V.出版
Nested Sampling (NS) is a parameter space sampling algorithm which can be used for sampling the equilibrium thermodynamics of atomistic systems. NS has previously been used to explore the potential energy surface of a coarse-grained protein model and has significantly outperformed parallel tempering when calculating heat capacity curves of Lennard-Jones clusters. The original NS algorithm uses Monte Carlo (MC) moves; however, a variant, Galilean NS, has recently been introduced which allows NS to be incorporated into a molecular dynamics framework, so NS can be used for systems which lack efficient prescribed MC moves. In this work we demonstrate the applicability of Galilean NS to atomistic systems. We present an implementation of Galilean NS using the Amber molecular dynamics package and demonstrate its viability by sampling alanine dipeptide, both in vacuo and implicit solvent. Unlike previous studies of this system, we present the heat capacity curves of alanine dipeptide, whose calculation provides a stringent test for sampling algorithms. We also compare our results with those calculated using replica exchange molecular dynamics (REMD) and find good agreement. We show the computational effort required for accurate heat capacity estimation for small peptides. We also calculate the alanine dipeptide Ramachandran free energy surface for a range of temperatures and use it to compare the results using the latest Amber force field with previous theoretical and experimental results. (C) 2016 The Authors. Published by Elsevier B.V.