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Robosample: A rigid-body molecular simulation program based on robot mechanics.
Biochimica et Biophysica Acta (BBA) - General Subjects ( IF 2.8 ) Pub Date : 2020-04-13 , DOI: 10.1016/j.bbagen.2020.129616 Laurentiu Spiridon 1 , Teodor Asvadur Şulea 1 , David D L Minh 2 , Andrei-Jose Petrescu 1
Biochimica et Biophysica Acta (BBA) - General Subjects ( IF 2.8 ) Pub Date : 2020-04-13 , DOI: 10.1016/j.bbagen.2020.129616 Laurentiu Spiridon 1 , Teodor Asvadur Şulea 1 , David D L Minh 2 , Andrei-Jose Petrescu 1
Affiliation
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BACKGROUND
Compared with all-atom molecular dynamics (MD), constrained MD methods allow for larger time steps, potentially reducing computational cost. For this reason, there has been continued interest in improving constrained MD algorithms to increase configuration space sampling in molecular simulations.
METHODS
Here, we introduce Robosample, a software package that implements high-performance constrained dynamics algorithms, originally developed for robotics, and applies them to simulations of biomolecular systems. As in the gMolmodel package developed by Spiridon and Minh in 2017, Robosample uses Constrained Dynamics Hamiltonian Monte Carlo (CDHMC) as a Gibbs sampling move - a type of Monte Carlo move where a subset of coordinates is allowed to change. In addition to the previously described Cartesian and torsional dynamics moves, Robosample implements spherical and cylindrical joints that can be distributed along the molecule by the user.
RESULTS
In alanine dipeptide simulations, the free energy surface is recovered by mixing fully flexible with torsional, cylindrical, or spherical dynamics moves. Ramachandran dynamics, where only the two key torsions are mobile, accelerate the slowest transition by an order of magnitude. We also show that simulations of a complex glycan cover significantly larger regions of the configuration space when mixed with constrained dynamics.
MAJOR CONCLUSIONS
Robosample is a tool of choice for efficient conformational sampling of large biomolecules.
GENERAL SIGNIFICANCE
Robosample is intended as a reliable and user-friendly simulation package for fast biomolecular sampling that does not require extensive expertise in mechanical engineering or in the statistical mechanics of reduced coordinates.
中文翻译：
Robosample：基于机器人力学的刚体分子模拟程序。
背景技术与全原子分子动力学（MD）相比，受约束的MD方法允许更大的时间步长，从而有可能降低计算成本。因此，人们一直对改进约束MD算法以增加分子模拟中的配置空间采样感兴趣。方法在这里，我们介绍Robosample，该软件包最初是为机器人技术而开发的，该软件包实现了高性能的约束动力学算法，并将其应用于生物分子系统的仿真。正如Spiridon和Minh在2017年开发的gMolmodel软件包中一样，Robosample使用约束动力学汉密尔顿蒙特卡洛（CDHMC）作为吉布斯采样移动-一种允许更改坐标子集的蒙特卡洛移动。除了前面描述的笛卡尔动力学和扭转动力学运动之外，Robosample实现了球形和圆柱形接头，用户可以沿着分子分布它们。结果在丙氨酸二肽模拟中，通过将完全柔性与扭转，圆柱或球形动力学运动混合来恢复自由能表面。Ramachandran动力学只有两个关键扭转是可移动的，从而将最慢的过渡速度提高了一个数量级。我们还显示，当与受约束的动力学混合时，复杂聚糖的模拟会覆盖配置空间的较大区域。主要结论Robosample是对大型生物分子进行有效构象采样的首选工具。
更新日期：2020-04-13
中文翻译：
Robosample：基于机器人力学的刚体分子模拟程序。
背景技术与全原子分子动力学（MD）相比，受约束的MD方法允许更大的时间步长，从而有可能降低计算成本。因此，人们一直对改进约束MD算法以增加分子模拟中的配置空间采样感兴趣。方法在这里，我们介绍Robosample，该软件包最初是为机器人技术而开发的，该软件包实现了高性能的约束动力学算法，并将其应用于生物分子系统的仿真。正如Spiridon和Minh在2017年开发的gMolmodel软件包中一样，Robosample使用约束动力学汉密尔顿蒙特卡洛（CDHMC）作为吉布斯采样移动-一种允许更改坐标子集的蒙特卡洛移动。除了前面描述的笛卡尔动力学和扭转动力学运动之外，Robosample实现了球形和圆柱形接头，用户可以沿着分子分布它们。结果在丙氨酸二肽模拟中，通过将完全柔性与扭转，圆柱或球形动力学运动混合来恢复自由能表面。Ramachandran动力学只有两个关键扭转是可移动的，从而将最慢的过渡速度提高了一个数量级。我们还显示，当与受约束的动力学混合时，复杂聚糖的模拟会覆盖配置空间的较大区域。主要结论Robosample是对大型生物分子进行有效构象采样的首选工具。
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