MOLECULAR DYNAMICS SIMULATIONS & METHOD DEVELOPMENT

计算机图形实验室的设施被用来显示 并分析分子动力学模拟结果。 我们的研究 项目的重点是a）进一步完善和测试新一代 附加和非附加力场参数，用于 分子力学和动力学计算，和B）大分子 模拟使用分子动力学。 新的琥珀力场 在分子动力学模拟中进行了广泛的测试， 分子，特别关注DNA模拟。 奔放 分子动力学模拟已被应用于模拟 脱氧核糖十二聚体双链体d（CGCGAATTCGCG）2及其氨基磷酸酯 (N-P)水溶液中的模拟物。 计算发现，3' 氨基磷酸酯修饰的DNA双链体经历B到A的转变 而正常的DNA是A到B的转变，这证实了实验结果。 观察并证明了新的琥珀力场的质量 参数化 新的AMBER参数化方法被应用于研究 小分子的构象平衡。 琥珀 参数化正在扩展到包括非加性效应， 孤对相互作用

The Computer Graphics Laboratory facilities were used to display and analyze molecular dynamics simulations results. Our research projects focus on a) further refining and testing the new generation of additive and nona dditive force field parameters to be used in molecular mechanics and dynamics calculations, and b) macromolecular simulation using molecular dynamics. The new AMBER force field was extensively tested in molecular dynamics simulations for large molecules, with special focus on DNA simulation. Unrestrained molecular dynamics simulations have been applied to simulate deoxyribose dodecamer duplex d(CGCGAATTCGCG)2 and its phosphoramidate (N-P) analog in water solution. The calculations find that 3' phosphoramidate modified DNA duplexes undergo a B to A transition whereas normal DNA an A to B transition, which confirms experimental observation and proves the quality of the new AMBER force field parametrization. New AMBER parametrization has been applied to study conformational equilibria of small molecules. The AMBER parametrization is being extended to include nonadditive effects and lone pairs interactions.