Effect of warmup protocol and sampling time on convergence of molecular dynamics simulations of a DNA dodecamer using...

This report describes one 3000 ps and two 1500 ps molecular dynamic simulations on a TATA box containing dodecamer DNA duplex in a periodic box of TIP3P water molecules, using the AMBER 4.1 implementation of the particle-mesh Ewald method. We compare the effect of warmup protocol and simulation time length on the root-mean square deviation (RMSD) parameter. For the longer simulation, the RMSD computed for the 500-1000 ps time interval is representative of longer time intervals, including 500-3000 ps. The various warmup protocols do not appear to have a significant effect on the simulation results. Based on the present results, DNA sequence-dependent differences in RMSD, or related properties, should exceed two standard deviations before being attributed to non-simulation factors, such as warmup protocol and sampling time effects; we recommend a minimum criterion of at least a three standard deviation difference with a sampling period of at least 500-1000 ps. In addition, while end effects appear negligible there is a consistent dependence of RMSD on DNA helix length.