Implementation of Accelerated Molecular Dynamics in NAMD.
Implementation of Accelerated Molecular Dynamics in NAMD.
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DOI：
10.1088/1749-4699/4/1/015002
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发表时间：
2011-01-01
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通讯作者：
McCammon, J Andrew
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作者：
Wang, Yi;Harrison, Christopher B;McCammon, J Andrew
加速分子动力学 (aMD) 是一种增强采样方法，通过减少分隔系统不同状态的能垒来改进构象空间采样。这里我们介绍aMD在并行仿真程序NAMD中的实现。我们表明，与经典 MD 模拟相比，使用 NAMD 执行的 aMD 模拟只需很小的开销。通过丙氨酸二肽的示例应用，我们讨论了加速参数的选择、aMD 结果的解释以及 aMD 方法的优点和局限性。
Accelerated molecular dynamics (aMD) is an enhanced-sampling method that improves the conformational space sampling by reducing energy barriers separating different states of a system. Here we present the implementation of aMD in the parallel simulation program NAMD. We show that aMD simulations performed with NAMD have only a small overhead compared with classical MD simulations. Through example applications to the alanine dipeptide, we discuss the choice of acceleration parameters, the interpretation of aMD results, as well as the advantages and limitations of the aMD method.