Bergonzo Christina, Campbell Arthur J, Walker Ross C, Simmerling Carlos
Department of Chemistry, State University of New York at Stony Brook, Stony Brook, NY 11794-3400.
Int J Quantum Chem. 2009 Aug 27;109(15):3781. doi: 10.1002/qua.22405.
The nudged elastic band method (NEB) can be used to find a minimum energy path between two given starting structures. This method has been available in the standard release of the Amber9 and Amber10 suite of programs. In this paper a novel implementation of this method will be discussed, in which the nudged elastic band method is applied to only a specific, user-defined subset of atoms in a particular system, returning comparable results and minimum energy pathways as the standard implementation for an alanine dipeptide test system. This allows incorporation of explicit solvent with simulated systems, which may be preferred in many cases to an implicit solvent model. From a computational standpoint, this implementation of NEB also reduces the communication overhead inside the code, resulting in better performance for larger systems.
推挤弹性带方法（NEB）可用于找到两个给定起始结构之间的最小能量路径。该方法已在Amber9和Amber10程序套件的标准版本中可用。本文将讨论该方法的一种新颖实现方式，其中推挤弹性带方法仅应用于特定系统中特定的、用户定义的原子子集，对于丙氨酸二肽测试系统，其返回的结果和最小能量路径与标准实现方式相当。这使得在模拟系统中能够纳入显式溶剂，在许多情况下，这可能比隐式溶剂模型更可取。从计算角度来看，NEB的这种实现方式还减少了代码内部的通信开销，从而在处理更大系统时具有更好的性能。
