Institute of Physical and Theoretical Chemistry, J. W. Goethe University, Max-von-Laue-Str. 7, D-60438 Frankfurt, Germany.
J Chem Phys. 2010 Apr 14;132(14):144109. doi: 10.1063/1.3369626.
We propose an efficient and simple method for fast conformational sampling by introducing the solvent viscosity as a parameter to the conventional temperature replica exchange molecular dynamics (T-REMD) simulation method. The method, named V-REMD (V stands for viscosity), uses both low solvent viscosity and high temperature to enhance sampling for each replica; therefore it requires fewer replicas than the T-REMD method. To reduce the solvent viscosity by a factor of lambda in a molecular dynamics simulation, one can simply reduce the mass of solvent molecules by a factor of lambda(2). This makes the method as simple as the conventional method. Moreover, thermodynamic and conformational properties of structures in replicas are still useful as long as one has sufficiently sampled the Boltzmann ensemble. The advantage of the present method has been demonstrated with the simulations of the trialanine, deca-alanine, and a 16-residue beta-hairpin peptides. It shows that the method could reduce the number of replicas by a factor of 1.5 to 2 as compared with the T-REMD method.
我们提出了一种高效、简单的快速构象采样方法，通过将溶剂粘度作为参数引入到传统的温度复制交换分子动力学（T-REMD）模拟方法中。该方法名为 V-REMD（V 代表粘度），它在每个副本中同时使用低溶剂粘度和高温来增强采样；因此，它比 T-REMD 方法需要更少的副本。在分子动力学模拟中，要将溶剂粘度降低到 lambda 的因子，可以简单地将溶剂分子的质量降低到 lambda(2)的因子。这使得该方法与传统方法一样简单。此外，只要充分采样了玻尔兹曼系综，副本中结构的热力学和构象性质仍然是有用的。本方法的优点已通过三肽、十肽和 16 残基β发夹肽的模拟得到证明。与 T-REMD 方法相比，该方法可以将副本数量减少 1.5 到 2 倍。
