CHARMM-GUI Polymer Builder for Modeling and Simulation of Synthetic Polymers.
CHARMM-GUI Polymer Builder for Modeling and Simulation of Synthetic Polymers.
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DOI：
10.1021/acs.jctc.1c00169
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发表时间：
2021-04-13
影响因子：
5.5
通讯作者：
Im W
中科院分区：
文献类型：
--
作者：
Choi YK;Park SJ;Park S;Kim S;Kern NR;Lee J;Im W
分子建模和模拟是聚合物科学和工程的宝贵工具，它们预测聚合物的物理化学性质，并在分子水平上深入了解其潜在的机理。然而，由于结构以及长度和时间尺度的巨大变化，构建现实的聚合物系统是具有挑战性的，需要相当多的经验。这项工作描述了CHARMM-图形用户界面(http://www.charmm-gui.org/input/polymer)，)中的聚合物生成器，这是一个基于网络的基础设施，提供了一个通用的和自动化的过程来构建一个宽松的聚合物系统。聚合物生成器不仅提供了多种建模方法来构建复杂的聚合物结构，而且通过内置的粗粒度模型和全原子替换生成了逼真的聚合物熔体和溶液系统。用各种实验数据和全原子模拟对粗粒度模型参数化进行了推广和广泛的验证。此外，通过34个均聚物熔体体系的密度计算、170个均聚物熔体体系的特征比计算、聚(苯乙烯-b-甲基丙烯酸甲酯)嵌段共聚物的形态图以及两亲聚(环氧乙烷-b-乙基乙烷)嵌段共聚物在水中的自组装行为，证明了Polmer Builder产生松弛聚合物体系的能力。我们希望Polmer Builder有助于开展创新和新颖的聚合物建模和模拟研究，以深入了解复杂含聚合物体系的结构、动力学和潜在机制。
Molecular modeling and simulations are invaluable tools for polymer science and engineering, which predict physicochemical properties of polymers and provide molecular-level insight into the underlying mechanisms. However, building realistic polymer systems is challenging and requires considerable experience because of great variations in structures as well as length and time scales. This work describes Polymer Builder in CHARMM-GUI (http://www.charmm-gui.org/input/polymer), a web-based infrastructure that provides a generalized and automated process to build a relaxed polymer system. Polymer Builder not only provides versatile modeling methods to build complex polymer structures, but also generates realistic polymer melt and solution systems through the built-in coarse-grained model and all-atom replacement. The coarse-grained model parameterization is generalized and extensively validated with various experimental data and all-atom simulations. In addition, the capability of Polymer Builder for generating relaxed polymer systems is demonstrated by density calculations of 34 homopolymer melt systems, characteristic ratio calculations of 170 homopolymer melt systems, a morphology diagram of poly(styrene-b-methyl methacrylate) block copolymers, and self-assembly behavior of amphiphilic poly(ethylene oxide-b-ethyl ethane) block copolymers in water. We hope that Polymer Builder is useful to carry out innovative and novel polymer modeling and simulation research to acquire insight into structures, dynamics, and underlying mechanisms of complex polymer-containing systems.
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影响因子：
4.4
作者：
Grest, GS;Lacasse, MD;Gupta, AM
通讯作者：
Gupta, AM
影响因子：
56.9
作者：
Discher, BM;Won, YY;Hammer, DA
通讯作者：
Hammer, DA
影响因子：
4.4
作者：
Chremos, Alexandros;Nikoubashman, Arash;Panagiotopoulos, Athanassios Z.
通讯作者：
Panagiotopoulos, Athanassios Z.
影响因子：
4.3
作者：
Eastman P;Swails J;Chodera JD;McGibbon RT;Zhao Y;Beauchamp KA;Wang LP;Simmonett AC;Harrigan MP;Stern CD;Wiewiora RP;Brooks BR;Pande VS
通讯作者：
Pande VS
影响因子：
3.4
作者：
Fortunato, Michael E.;Colina, Coray M.
通讯作者：
Colina, Coray M.