Atomistic Force Fields for Proteins
Atomistic Force Fields for Proteins
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DOI：
10.1007/978-1-4939-9608-7_1
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发表时间：
2019-01-01
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影响因子：
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通讯作者：
Best, Robert B.
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文献类型：
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作者：
Best, Robert B.
用于蛋白质分子动力学（MD）模拟的全原子经典力场目前在计算模型的宇宙中占据了最佳位置，足够详细，在许多情况下具有预测价值，但也足够简单，现在可以通过专门的硬件或增强的采样方法对一些生物相关的时间尺度（微秒或更长）进行采样。然而，由于它们漫长的进化历史，现在有无数的力场分支在当前使用，这可能使那些进入仿真领域的人很难知道哪一组参数是给定应用的最佳参数。在这一章中，我试图概述不同力场的历史动机，建议如何确定最合适的模型，以及如果结果与实验证据相冲突该怎么办。
All-atom, classical force fields for protein molecular dynamics (MD) simulations currently occupy a sweet spot in the universe of computational models, sufficiently detailed to be of predictive value in many cases, yet also simple enough that some biologically relevant time scales (microseconds or more) can now be sampled via specialized hardware or enhanced sampling methods. However, due to their long evolutionary history, there is now a myriad of force field branches in current use, which can make it hard for those entering the simulation field to know which would be the best set of parameters for a given application. In this chapter, I try to give an overview of the historical motivation for the different force fields available, suggestions for how to determine the most appropriate model and what to do if the results are in conflict with experimental evidence.