Loncharich R J, Brooks B R
Molecular Graphics and Simulation Laboratory, National Institutes of Health, Bethesda, Maryland 20892.
Proteins. 1989;6(1):32-45. doi: 10.1002/prot.340060104.
This paper considers the effects of truncating long-range forces on protein dynamics. Six methods of truncation that we investigate as a function of cutoff criterion of the long-range potentials are (1) a shifted potential; (2) a switching function; (3) simple atom-atom truncation based on distance; (4) simple atom-atom truncation based on a list which is updated periodically (every 25 steps); (5) simple group-group truncation based on distance; and (6) simple group-group truncation based on a list which is updated periodically (every 25 steps). Based on 70 calculations of carboxymyoglobin we show that the method and distance of long range cutoff have a dramatic effect on overall protein behavior. Evaluation of the different methods is based on comparison of a simulation's rms fluctuation about the average coordinates, the rms deviation from the average coordinates of a no cutoff simulation and from the X-ray structure of the protein. The simulations in which long-range forces are truncated by a shifted potential shows large rms deviations for cutoff criteria less than 14 A, and reasonable deviations and fluctuations at this cutoff distance or larger. Simulations using a switching function are investigated by varying the range over which electrostatic interactions are switched off. Results using a short switching function that switches off the potential over a short range of distances are poor for all cutoff distances. A switching function over a 5-9 A range gives reasonable results for a distance-dependent dielectric, but not using a constant dielectric. Both the atom-atom and group-group truncation methods based on distance shows large rms deviation and fluctuation for short cutoff distances, while for cutoff distances of 11 A or greater, reasonable results are achieved. Although comparison of these to distance-based truncation methods show surprisingly larger rms deviations for the group-group truncation, contrary to simulation studies of aqueous ionic solutions. The results of atom-atom or group-group list-based simulations generally appear to be less stable than the distance-based simulations, and require more frequent velocity scaling or stronger coupling to a heat bath.
本文考虑了截断长程力对蛋白质动力学的影响。我们研究了六种截断方法，它们是长程势截断标准的函数，分别为：(1) 移位势；(2) 切换函数；(3) 基于距离的简单原子-原子截断；(4) 基于定期（每25步）更新的列表的简单原子-原子截断；(5) 基于距离的简单基团-基团截断；(6) 基于定期（每25步）更新的列表的简单基团-基团截断。基于对羧基肌红蛋白的70次计算，我们表明长程截断的方法和距离对蛋白质的整体行为有显著影响。对不同方法的评估基于模拟相对于平均坐标的均方根波动、与无截断模拟的平均坐标以及与蛋白质X射线结构的平均坐标的均方根偏差的比较。对于截断标准小于14 Å的情况，采用移位势截断长程力的模拟显示出较大的均方根偏差，而在该截断距离或更大时，偏差和波动较为合理。通过改变静电相互作用关闭的范围来研究使用切换函数的模拟。对于所有截断距离，使用在短距离范围内关闭势的短切换函数得到的结果都很差。对于距离依赖的介电常数，在5 - 9 Å范围内的切换函数给出了合理的结果，但对于恒定介电常数则不然。基于距离的原子-原子和基团-基团截断方法在短截断距离时均显示出较大的均方根偏差和波动，而对于11 Å或更大的截断距离，则可得到合理的结果。尽管将这些方法与基于距离的截断方法进行比较时，基团-基团截断显示出惊人的更大均方根偏差，这与水离子溶液的模拟研究相反。基于原子-原子或基团-基团列表的模拟结果通常似乎不如基于距离的模拟稳定，并且需要更频繁的速度缩放或更强的与热浴的耦合。
