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Coarse-Grained Molecular Dynamics Force-Field for Polyacrylamide in Infinite Dilution Derived from Iterative Boltzmann Inversion and MARTINI Force-Field
The Journal of Physical Chemistry B ( IF 2.8 ) Pub Date : 2018-01-18 00:00:00 , DOI: 10.1021/acs.jpcb.7b09019 Pallavi Banerjee 1, 2 , Sudip Roy 1 , Nitish Nair 1
The Journal of Physical Chemistry B ( IF 2.8 ) Pub Date : 2018-01-18 00:00:00 , DOI: 10.1021/acs.jpcb.7b09019 Pallavi Banerjee 1, 2 , Sudip Roy 1 , Nitish Nair 1
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We present a mesoscale model of aqueous polyacrylamide in the infinitely dilute concentration regime, by combining an extant coarse-grained (CG) force-field, MARTINI, and the Iterative Boltzmann Inversion protocol (IBI). MARTINI force-field was used to retain the thermodynamics of solvation of the polymer in water, whereas the structural properties and intrapolymer interactions were optimized by IBI. Atomistic molecular dynamics simulations of polymer in water were performed to benchmark the mesoscale simulations. Our results from the CG model show excellent agreement in structure with the atomistic system. We also studied the dynamical behavior of our CG system by computing the shear viscosity and compared it with the standard IBI model. The viscosity trends of our model were similar to the atomistic system, whereas the standard IBI model was highly dissimilar as expected. In summary, our hybrid CG model sufficiently mimics an infinitely dilute system, and is superior to both MARTINI and IBI in representing the structure and thermodynamics of the atomistic system, respectively. Our hybrid coarse-graining strategy promises applicability in large-scale simulations of polymeric/biological systems where the structure needs to be replicated accurately while preserving the thermodynamics of a smoother surrounding.
中文翻译：
迭代稀释玻尔兹曼反演和MARTINI力场衍生的无限稀释聚丙烯酰胺的粗粒分子动力学力场
通过结合现存的粗粒度（CG）力场，MARTINI和迭代玻耳兹曼反演协议（IBI），我们在无限稀的浓度范围内提出了聚丙烯酰胺水溶液的中尺度模型。MARTINI力场用于保留聚合物在水中的溶剂化热力学，而结构特性和聚合物内相互作用则通过IBI进行了优化。进行了聚合物在水中的原子分子动力学模拟，以对中尺度模拟进行基准测试。我们从CG模型获得的结果表明，该结构与原子系统具有极好的一致性。我们还通过计算剪切粘度研究了CG系统的动力学行为，并将其与标准IBI模型进行了比较。我们模型的粘度趋势类似于原子体系，而标准IBI模型与预期的非常不同。总而言之，我们的混合CG模型足以模拟无限稀释的系统，并且在表示原子系统的结构和热力学方面分别优于MARTINI和IBI。我们的混合粗粒度策略保证了在聚合物/生物系统的大规模仿真中的适用性，在该仿真中，结构需要精确复制，同时又要保持较光滑环境的热力学。
更新日期：2018-01-18
中文翻译：
迭代稀释玻尔兹曼反演和MARTINI力场衍生的无限稀释聚丙烯酰胺的粗粒分子动力学力场
通过结合现存的粗粒度（CG）力场，MARTINI和迭代玻耳兹曼反演协议（IBI），我们在无限稀的浓度范围内提出了聚丙烯酰胺水溶液的中尺度模型。MARTINI力场用于保留聚合物在水中的溶剂化热力学，而结构特性和聚合物内相互作用则通过IBI进行了优化。进行了聚合物在水中的原子分子动力学模拟，以对中尺度模拟进行基准测试。我们从CG模型获得的结果表明，该结构与原子系统具有极好的一致性。我们还通过计算剪切粘度研究了CG系统的动力学行为，并将其与标准IBI模型进行了比较。我们模型的粘度趋势类似于原子体系，而标准IBI模型与预期的非常不同。总而言之，我们的混合CG模型足以模拟无限稀释的系统，并且在表示原子系统的结构和热力学方面分别优于MARTINI和IBI。我们的混合粗粒度策略保证了在聚合物/生物系统的大规模仿真中的适用性，在该仿真中，结构需要精确复制，同时又要保持较光滑环境的热力学。
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