THE EFFECTS OF TRUNCATING LONG RANGE FORCES ON PROTEIN DYNAMICS

截断长程力对蛋白质动力学的影响

• 批准号: 3896410
• 负责人: R J LONCHARICH
• 金额: --
• 依托单位: CENTER FOR INFORMATION TECHNOLOGY
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/3896410
• 关键词: chemical bond; chemical models; computer graphics /printing; computer simulation; electron density; hemoprotein structure; mathematical model; molecular dynamics; myoglobin; protein structure

We have carried out a basic research project that considers the effects of truncating long range forces on protein dynamics. Based on seventy calculations of carboxymyoglobin we have shown that the method and distance of long range cutoff have a dramatic effect on overall protein behavior. The simulations in which long range forces are truncated by a shifted potential shows large rms deviations for cutoff criteria less than 14 Angstroms, and reasonable deviations and fluctuations at this cutoff distance or larger. Simulations using a switching function were 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 Angstrom range gives reasonable results for a distant 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 Angstroms or greater, reasonable results are achieved. Although comparison of these to distance based truncation methods show surprisingly large rms deviations for the group-group truncation, contrary to 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 heatbath. We hope that the results of these simulations provide assistance in choosing a method of truncating long range potentials in protein dynamics.

我们开展了一项基础研究项目，考虑了以下因素的影响： 截断对蛋白质动力学的长程力。以七十为基础 碳氧肌红蛋白的计算我们已经证明了该方法和 长程截止距离对整体蛋白质有巨大影响 行为。长程力被截断的模拟 转移电位显示截止标准的较大均方根偏差小于 14 埃，以及此截止点的合理偏差和波动 距离或更大。使用开关函数的模拟是 通过改变静电相互作用的范围进行研究 已关闭。使用短开关函数的结果 短距离内的切断潜力对于所有切断来说都很差 距离。 5--9 埃范围内的开关函数给出 远距离相关电介质的合理结果，但不使用 恒定的介电常数。原子-原子和基团-基团截断方法 基于距离显示较大的均方根偏差和短期波动 截止距离，而对于 11 埃或更大的截止距离， 取得了合理的结果。尽管将这些与距离进行比较 基于截断的方法显示出惊人的大均方根偏差 基团截断，与离子水溶液的研究相反。 通常基于原子-原子或基团-基团列表的模拟结果 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与热浴的更强耦合。我们希望 这些模拟的结果有助于选择 截断蛋白质动力学中长程势的方法。