Wales David J
Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK.
Phys Biol. 2005 Nov 9;2(4):S86-93. doi: 10.1088/1478-3975/2/4/S02.
Thermodynamic and dynamic properties of biomolecules can be calculated using a coarse-grained approach based upon sampling stationary points of the underlying potential energy surface. The superposition approximation provides an overall partition function as a sum of contributions from the local minima, and hence functions such as internal energy, entropy, free energy and the heat capacity. To obtain rates we must also sample transition states that link the local minima, and the discrete path sampling method provides a systematic means to achieve this goal. A coarse-grained picture is also helpful in locating the global minimum using the basin-hopping approach. Here we can exploit a fictitious dynamics between the basins of attraction of local minima, since the objective is to find the lowest minimum, rather than to reproduce the thermodynamics or dynamics.
生物分子的热力学和动力学性质可以使用基于对潜在能量表面的驻点进行采样的粗粒度方法来计算。叠加近似提供了一个整体的配分函数，它是来自局部极小值贡献的总和，从而得出诸如内能、熵、自由能和热容等函数。为了获得速率，我们还必须对连接局部极小值的过渡态进行采样，而离散路径采样方法提供了实现这一目标的系统手段。粗粒度图景对于使用盆地跳跃方法定位全局极小值也很有帮助。在这里，我们可以利用局部极小值吸引盆之间的虚拟动力学，因为目标是找到最低的极小值，而不是再现热力学或动力学。
