用MBN Explorer研究生物系统中的化学反应：用动力学拓扑实现分子力学
Studying chemical reactions in biological systems with MBN Explorer: implementation of molecular mechanics with dynamical topology
摘要：
分子力学力场的概念在研究生物分子系统中的各种过程中已被广泛接受。在本文中，我们提出了一个修改的标准CHARMM力场，允许动态变化的分子拓扑结构的系统模拟。修改后的力场的实施进行了流行的程序MBN资源管理器，并支持的发展，我们提供了几个说明性的案例研究，动态拓扑是必要的。特别是，它表明，修改后的分子力学力场可以应用于研究过程中，化学键的断裂起着至关重要的作用，例如，在辐射或碰撞引起的损伤中，以及在涉及生物分子系统的转化和断裂过程中。
英文摘要：
The concept of molecular mechanics force field has been widely accepted nowadays for studying various processes in biomolecular systems. In this paper, we suggest a modification for the standard CHARMM force field that permits simulations of systems with dynamically changing molecular topologies. The implementation of the modified force field was carried out in the popular program MBN Explorer, and, to support the development, we provide several illustrative case studies where dynamical topology is necessary. In particular, it is shown that the modified molecular mechanics force field can be applied for studying processes where rupture of chemical bonds plays an essential role, e.g., in irradiation- or collision-induced damage, and also in transformation and fragmentation processes involving biomolecular systems.
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