MOLECULAR DYNAMICS SIMULATIONS AND METHOD DEVELOPMENT

该子项目是利用 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 中心，不一定是研究者的机构。 我们使用计算机图形实验室的设备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）精炼，测试和开发新一代的加性和非加性力场参数;和B）使用分子动力学的大分子模拟。 这项工作正在进行，以进一步发展加性和非加性琥珀力场。非加性AMBER参数化包括基于原子极化率和孤对相互作用的非加性效应。 提出了一种新的方法来处理分子内极化过程中的电荷发展的非加性模拟。 更彻底的测试已经在DNA和小蛋白质上进行了使用非加性力场与额外的偏心（孤对）点位于电子供体原子。此外，还对小蛋白如泛素和短聚丙氨酸肽进行了更多的测试。 最近，分子动力学模拟已经进行，以确定稳定性（自由能）和构象转变短RNA环：UUCG和UUUU。

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. 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.