Free energy simulations with the AMOEBA polarizable force field and metadynamics on GPU platform
Free energy simulations with the AMOEBA polarizable force field and metadynamics on GPU platform
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DOI：
10.1002/jcc.24227
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发表时间：
2016-03
影响因子：
3
通讯作者：
Xiangda Peng;Yuebin Zhang;Huiying Chu;Guohui Li
中科院分区：
文献类型：
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作者：
Xiangda Peng;Yuebin Zhang;Huiying Chu;Guohui Li
自由能计算库PLUMED已被纳入OpenMM仿真工具包，目的是在GPU平台上使用AMOEBA可极化力场执行增强的采样MD仿真。两个例子，（I）水对分离的自由能分布（II）丙氨酸二肽二面角自由能表面在显式溶剂中，在这里提供证明我们的实现的准确性和效率。当采用AMOEBA极化力场时，可以在可承受的MD模拟时间内获得收敛的自由能分布。此外，使用AMOEBA极化力场估计的自由能表面与实验数据和从头计算方法的计算结果一致。因此，在这项工作中的实现是可靠的，并将被用来研究更复杂的生物现象，在一个准确和有效的方式。© 2015 Wiley Periodicals，Inc.
The free energy calculation library PLUMED has been incorporated into the OpenMM simulation toolkit, with the purpose to perform enhanced sampling MD simulations using the AMOEBA polarizable force field on GPU platform. Two examples, (I) the free energy profile of water pair separation (II) alanine dipeptide dihedral angle free energy surface in explicit solvent, are provided here to demonstrate the accuracy and efficiency of our implementation. The converged free energy profiles could be obtained within an affordable MD simulation time when the AMOEBA polarizable force field is employed. Moreover, the free energy surfaces estimated using the AMOEBA polarizable force field are in agreement with those calculated from experimental data and ab initio methods. Hence, the implementation in this work is reliable and would be utilized to study more complicated biological phenomena in both an accurate and efficient way. © 2015 Wiley Periodicals, Inc.