与生物膜和生物大分子相关的很多生命进程是由热涨落驱动系统跨越势垒而形成的微观构象变化过程。这些需要跨越势垒的相变的稀有事件具有微观意义下极长的等待时间，因而需要采用伞抽样等自由能计算方法结合分子模拟来寻找迁移轨迹和计算迁移过程的自由能。自由能计算可以揭示相应构象迁移过程的各种特征，已被广泛应用。然而，在膜-肽相互作用等问题中,微观构象迁移复杂、自由度多等特点使得针对问题寻找合适的反应坐标具有本质的困难，从而严重的约束了自由能计算的应用。 申请人团队认识到使用不恰当的反应坐标进行伞抽样时总是存在构象跳跃，而这些构象跳跃可以用于寻找新的更合适的局部反应坐标，并在此基础上初步发展了多步伞抽样框架。这一计算框架已经在离子穿膜渗透等问题中获得了成功的应用。在本项目中，申请人将把这一计算框架用于膜-肽相互作用这一复杂而重要的问题中，通过自由能计算理解抗菌肽的抗菌机理和选择性的来源等重要问题。

In many life processes that are related to biomembranes or Biomacromolecules, microscopic configuration changes are driven by thermal fluctuations. Free energy calculation based on molecular dynamics simulation or Monte-Carlo simulation is important in studing the transition trajectories and understanding these processes. Free energy calculation methods, such as Umbrella Sampling, have been widely applied in the study of rare events. However, due to the complexity and the large degree of freedom in many microscopic life processes, there is an intrisic difficulty in finding proper reaction coordinates that are required in free energy calculation. We note that an inproper reaction coordinate always leads to a configuration jump in umbrella sampling and the comfiguration jump is usually an important hint in designing better reaction coordinates. Based on this observation,we have developed a multi-step method for umbrella sampling,in which the reaction coordinates are designed step by step making use of the configuration jumps. This method has been shown to be successful in the study of transmembrane permeation of ions. In this proposal, we will improve this method and apply it in the study of membrane-peptide interactions, aiming an deep understanding of the antimicrobial mechanism and selectivity of antimicrobial peptides.