MOLECULAR DYNAMICS SIMULATIONS AND METHOD DEVELOPMENT

这个子项目是利用资源的许多研究子项目之一。 由NIH/NCRR资助的中心拨款提供。对子项目的主要支持 子项目的首席调查员可能是由其他来源提供的， 包括美国国立卫生研究院的其他来源。为子项目列出的总成本可能 表示该子项目使用的中心基础设施的估计数量， 不是由NCRR赠款提供给次级项目或次级项目工作人员的直接资金。 我们使用计算机图形学实验室的设施来显示和分析分子动力学模拟结果。我们的研究项目集中在a)提炼、测试和开发新一代添加和非添加的力场参数；以及b)使用分子动力学进行大分子模拟。 这项工作正在进行中，以进一步开发添加和非添加琥珀力场。非加性琥珀参数化包括基于原子极化率的非加性效应和孤子对相互作用。提出了一种处理非加性模拟电荷发展过程中分子内极化的新方法。 在DNA和小蛋白质上进行了更彻底的测试，使用位于给电子原子上的额外偏心(孤对)点的非加性力场。此外，还对泛素和短聚丙氨酸肽等小蛋白进行了更多的测试。 最近，为了确定短RNA环UUCG和UUUU的稳定性(自由能)和构象转变，人们进行了分子动力学模拟。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. We use the Computer Graphics Laboratory facilities to display and analyze molecular dynamics simulation results. Our research projects focus on a) refining, testing and developing the new generation of additive and nonadditive force field parameters; and b) macromolecular simulation using molecular dynamics. The work is being carried out to further develop the additive and nonadditive AMBER force field. The nonadditive AMBER parametrization includes nonadditive effects, based on atomic polarizabilities, and lone pairs interactions. A new approach to treat intra-molecular polarization has been proposed during charge development for nonadditive simulations. More thorough tests have been performed on DNA and small proteins using nonadditive force field with additional off-center (lone pairs) points located on electron-donating atoms. Additionally more tests have been performed on small protein such as ubiquitin, and short polyalanine peptides. Recently, molecular dynamics simulations have been performed in order to determine stability (free energies) and conformational transitions in short RNA loops: UUCG and UUUU.