Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk, 80-308, Poland.
Faculty of Physics, Astronomy and Informatics, Institute of Physics, Nicolaus Copernicus University, Grudziadzka 5, Torun, 87-100, Poland.
J Comput Chem. 2017 Mar 30;38(8):553-562. doi: 10.1002/jcc.24685. Epub 2017 Jan 11.
In this article, an implementation of steered molecular dynamics (SMD) in coarse-grain UNited RESidue (UNRES) simulations package is presented. Two variants of SMD have been implemented: with a constant force and a constant velocity. The huge advantage of SMD implementation in the UNRES force field is that it allows to pull with the speed significantly lower than the accessible pulling speed in simulations with all-atom representation of a system, with respect to a reasonable computational time. Therefore, obtaining pulling speed closer to those which appear in the atomic force spectroscopy is possible. The newly implemented method has been tested for behavior in a microcanonical run to verify the influence of introduction of artificial constrains on keeping total energy of the system. Moreover, as time dependent artificial force was introduced, the thermostat behavior was tested. The new method was also tested via unfolding of the Fn3 domain of human contactin 1 protein and the I27 titin domain. Obtained results were compared with Gø-like force field, all-atom force field, and experimental results. © 2017 Wiley Periodicals, Inc.
本文提出了在粗粒 UNited RESidue（UNRES）模拟包中实现导向分子动力学（SMD）的方法。实现了两种 SMD 变体：恒力和恒速。SMD 在 UNRES 力场中的巨大优势在于，与系统全原子表示的模拟相比，它允许以比可访问的拉伸速度低得多的速度进行拉伸，而计算时间合理。因此，有可能获得更接近原子力光谱中出现的拉伸速度。新实现的方法已在微正则运行中进行了测试，以验证引入人为约束对保持系统总能量的影响。此外，由于引入了随时间变化的人工力，因此还测试了恒温器的行为。还通过人接触蛋白 1 的 Fn3 结构域和 I27 原肌球蛋白结构域的展开来测试新方法。将获得的结果与 Gø 样力场、全原子力场和实验结果进行了比较。©2017 威利父子公司。
