Davidchack Ruslan L, Handel Richard, Tretyakov M V
Department of Mathematics, University of Leicester, Leicester LE1 7RH, United Kingdom.
J Chem Phys. 2009 Jun 21;130(23):234101. doi: 10.1063/1.3149788.
We present a new method for isothermal rigid body simulations using the quaternion representation and Langevin dynamics. It can be combined with the traditional Langevin or gradient (Brownian) dynamics for the translational degrees of freedom to correctly sample the canonical distribution in a simulation of rigid molecules. We propose simple, quasisymplectic second-order numerical integrators and test their performance on the TIP4P model of water. We also investigate the optimal choice of thermostat parameters.
我们提出了一种使用四元数表示和朗之万动力学进行等温刚体模拟的新方法。它可以与传统的朗之万或梯度(布朗)动力学相结合,用于平动自由度,以便在刚性分子模拟中正确采样正则分布。我们提出了简单的、拟辛二阶数值积分器,并在水的TIP4P模型上测试了它们的性能。我们还研究了恒温器参数的最佳选择。