ACCURATE CRYSTAL MOLECULAR-DYNAMICS SIMULATIONS USING PARTICLE-MESH-EWALD - RNA DINUCLEOTIDES - APU AND GPC

Long molecular dynamics (MD) simulations for two crystal RNA dinucleot ides ApU (2.0 ns) and GpC (1.5 ns) were performed, starting from the c rystallographic positions of all heavy atoms in the crystals. By emplo ying the particle-mesh-Ewald algorithm [Darden et al., J. Chem. Phys. 98 (1993) 10089] to accommodate the long-range Coulomb interactions, h ighly accurate MD structures were obtained for both crystals. The inst antaneous root-mean-square positional deviations of the heavy atoms eq uilibrate at approximately 0.4 Angstrom for both systems, while the ex perimental and calculated temperature factors are comparable in size. These results describe the first successful crystal MD simulation of R NA molecules.