作者Author: rpestana94 时间: 2024-4-11 22:12
1. About the time of simulation, depends of the systems, but you can check stability of the system using RMSD and visually check how is the behavior of the system. Although I will recommend to do at least 500 ns.
Using gmx_MMPBSA you can define the frames to be consider in the calculation using startframe and endframe variables.
2. About the interaction sites maybe you can try with ProLIF which is a python library to do this kind of analysis. 作者Author: sobereva 时间: 2024-4-12 05:52
1 取决于蛋白二聚体的特征。比如二聚体呈现显著的刚性，那么只取达到平衡后的一小段轨迹跑出来的平均相互作用能就已经准确了，此时再进一步延长也不会使得时间平均的结果有显著变化。反之，如果两个蛋白结合后会出现显著又很缓慢的构象变化，300ns都可能未必达到真正平衡，就更别提算准结合自由能了。具体是什么情况，可利用RMSD曲线等方式判断二聚体结构动力学特征。