Wang Yi, Harrison Christopher B, Schulten Klaus, McCammon J Andrew
Center for Theoretical Biological Physics, Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, Department of Pharmacology, University of California, San Diego, La Jolla, 92093, USA.
Comput Sci Discov. 2011;4(1). doi: 10.1088/1749-4699/4/1/015002.
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.
加速分子动力学（aMD）是一种增强采样方法，它通过降低分隔系统不同状态的能量壁垒来改善构象空间采样。在此，我们展示了aMD在并行模拟程序NAMD中的实现。我们表明，与经典分子动力学（MD）模拟相比，使用NAMD进行的aMD模拟仅具有很小的额外开销。通过对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方法的优缺点。
