METHODS AND APPLICATIONS OF HYBRID QM/MM SIMULATIONS TO BIOMOLECULAR SYSTEMS, S

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 研讨会将探索模拟酶反应的计算方法。本课程将介绍相关的理论背景，包括从头算和半经验分子轨道方法、密度泛函理论、分子力学力场、量子力学/分子力学混合势能函数以及在高性能计算机上的模拟技术。将主要使用迪纳摩文库进行案例研究，以确定气相、水中(使用隐式和显式溶剂)和酶活性部位的反应的自由能分布。有迪纳摩的经验是有帮助的，但不是参加的先决条件。 该研讨会是为计算生物物理学和物理有机化学方面的研究生、博士后研究人员和教职员工设计的，他们对计算化学方法有一些经验，并试图提高他们的能力，包括酶反应的建模。鼓励与会者在研讨会期间根据自己的研究讨论和研究生物分子系统。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The workshop will explore computational approaches for the simulation of enzymatic reactions. The course will present the relevant theoretical background including ab initio and semiempirical molecular orbital methods, density functional theory, molecular mechanics force fields, hybrid Quantum Mechanical/Molecular Mechanical potential energy functions, and simulation techniques on high performance computers. Case studies based on determining the free energy profile for a reaction in the gas phase, in water (using both implicit and explicit solvent) and in an enzyme active site will be presented using primarily the DYNAMO library. Experience with DYNAMO is helpful but not a prerequisite for attendance. The workshop is designed for graduate students, post-doctoral researchers and faculty in computational biophysics and physical organic chemistry who have some experience with computational chemistry methods and seek to enhance their capabilities to include the modeling of enzymatic reactions. Participants are encouraged to discuss and work on biomolecular systems from their own research during the workshop.