Modern Computational Methodology Applied to the Simulation of Blocked Trialanine Peptide in Vacuo, Water Clusters, and Bulk Water
Modern Computational Methodology Applied to the Simulation of Blocked Trialanine Peptide in Vacuo, Water Clusters, and Bulk Water
复制标题
现代计算方法应用于真空、水簇和大量水中封闭三丙氨酸肽的模拟
DOI：
10.1021/jp9704269
复制
发表时间：
1997
影响因子：
3.3
通讯作者：
G. Martyna
中科院分区：
文献类型：
--
作者：
S. Samuelson;D. Tobias;G. Martyna
报告了使用现代计算方法在 T = 300 K 下在散装计算机水中溶剂化、在计算机水簇中溶剂化以及在真空（隔离模型分子）中的 CH3CO−(Ala)3−NHCH3 溶剂化的计算机模拟研究结果。模拟是使用新的多用途分子动力学软件包 PINY MD 进行的，该软件包利用最近开发的模拟技术，能够以 6 fs 的积分时间步长（通常值的 6 倍）进化肽-水系统。具体地，以N端保护基团的羰基氧与C端保护基团的酰胺氢之间的距离为反应坐标，通过伞式采样计算肽的构象自由能面。对使用几种不同力场获得的结果进行比较：CHARMM22（MacKerell, A. D., Jr.；等人，未发表）、CHARMM19（Brooks, B., et al. J. Comput. Chem 1983, 4, 187.）和 AMBER95（Cornell 等人 J. Am. Chem. Soc. 1...
The results of computer simulation studies of CH3CO−(Ala)3−NHCH3 solvated in bulk computer water, solvated in computer water clusters, and in vacuo (isolated model molecule) at T = 300 K using modern computational methods are reported. The simulations were performed using a new multipurpose molecular dynamics package, PINY MD, which utilizes recently developed simulation techniques and is capable of evolving the peptide−water system with an integration time step of 6 fs, 6 times the usual value. Specifically, the conformational free energy surface of the peptide is calculated via umbrella sampling using the distance between the carbonyl oxygen of the N-terminal blocking group and the amide hydrogen of the C-terminal blocking group as the reaction coordinate. Comparisons are made between results obtained using the several different force fields, CHARMM22 (MacKerell, A. D., Jr.; et al., unpublished), CHARMM19 (Brooks, B., et al. J. Comput. Chem 1983, 4, 187.) and AMBER95 (Cornell et al. J. Am. Chem. Soc. 1...