Constant-pH molecular dynamics using stochastic titration
Constant-pH molecular dynamics using stochastic titration
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DOI：
10.1063/1.1497164
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发表时间：
2002-09-01
影响因子：
4.4
通讯作者：
Soares, CM
中科院分区：
文献类型：
--
作者：
Baptista, AM;Teixeira, VH;Soares, CM
提出了一种新的恒定pH分子动力学(MD)模拟方法，即pH为温度或压力等外部热力学参数的分子动力学模拟。在分子力学(MM)MD模拟期间，允许改变溶质中每个可滴定位置的质子化状态，新的质子化状态是通过连续介质静电学(CE)计算和质子化平衡的蒙特卡罗(MC)模拟的组合获得的。MM/MD和CE/MC算法之间的耦合是以一种确保适当的马尔可夫链的方式完成的，从预期的半正则分布进行抽样。将该随机滴定方法应用于琥珀酸的测定，旨在说明该方法，并考察其调节参数的选择。在不同pH值下，使用恒定pH分子动力学模拟，完全滴定琥珀酸，清楚地描绘了反式/古契异构化和质子化过程之间的耦合，使得有可能调和以前研究的一些明显相互矛盾的结果。与通常的MD方法相比，目前的恒pH MD方法所需的计算量略有增加。(C)2002年美国物理研究所。
A new method is proposed for performing constant-pH molecular dynamics (MD) simulations, that is, MD simulations where pH is one of the external thermodynamic parameters, like the temperature or the pressure. The protonation state of each titrable site in the solute is allowed to change during a molecular mechanics (MM) MD simulation, the new states being obtained from a combination of continuum electrostatics (CE) calculations and Monte Carlo (MC) simulation of protonation equilibrium. The coupling between the MM/MD and CE/MC algorithms is done in a way that ensures a proper Markov chain, sampling from the intended semigrand canonical distribution. This stochastic titration method is applied to succinic acid, aimed at illustrating the method and examining the choice of its adjustable parameters. The complete titration of succinic acid, using constant-pH MD simulations at different pH values, gives a clear picture of the coupling between the trans/gauche isomerization and the protonation process, making it possible to reconcile some apparently contradictory results of previous studies. The present constant-pH MD method is shown to require a moderate increase of computational cost when compared to the usual MD method. (C) 2002 American Institute of Physics.