Christen Markus, Christ Clara D, van Gunsteren Wilfred F
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zürich, Switzerland.
Chemphyschem. 2007 Jul 16;8(10):1557-64. doi: 10.1002/cphc.200700176.
A comparison of different treatments of bond-stretching interactions in molecular dynamics simulation is presented. Relative free energies from simulations using rigid bonds maintained with the SHAKE algorithm, using partially rigid bonds maintained with a recently introduced flexible constraints algorithm, and using fully flexible bonds are compared in a multi-configurational thermodynamic integration calculation of changing liquid water into liquid methanol. The formula for the free energy change due to a changing flexible constraint in a flexible constraint simulation is derived. To allow for a more direct comparison between these three methods, three different pairs of models for water and methanol were used: a flexible model (simulated without constraints and with flexible constraints), a rigid model (simulated with standard hard constraints), and an alternative flexible model (simulated with flexible constraints and standard hard constraints) in which the ideal or constrained bond lengths correspond to the average bond lengths obtained from a short simulation of the unconstrained flexible model. The particular treatment of the bonds induces differences of up to 2 % in the liquid densities, whereas (excess) free energy differences of up to 5.7 (4.3) kJ mol(-1) are observed. These values are smaller than the differences observed between the three different pairs of methanol/water models: up to 5 % in density and up to 8.5 kJ mol(-1) in (excess) free energy.
本文介绍了分子动力学模拟中键拉伸相互作用不同处理方法的比较。在将液态水转变为液态甲醇的多构型热力学积分计算中，比较了使用SHAKE算法维持刚性键、使用最近引入的柔性约束算法维持部分刚性键以及使用完全柔性键的模拟得到的相对自由能。推导了柔性约束模拟中由于柔性约束变化导致的自由能变化公式。为了更直接地比较这三种方法，使用了三对不同的水和甲醇模型：一个柔性模型（无约束和有柔性约束模拟）、一个刚性模型（标准硬约束模拟）以及一个替代柔性模型（柔性约束和标准硬约束模拟），其中理想或约束键长对应于无约束柔性模型短模拟得到的平均键长。键的特定处理在液体密度上导致高达2%的差异，而观察到（过量）自由能差异高达5.7（4.3）kJ mol⁻¹。这些值小于三对不同甲醇/水模型之间观察到的差异：密度差异高达5%，（过量）自由能差异高达8.5 kJ mol⁻¹。
