Effect of Warmup Protocol and Sampling Time on Convergence of Molecular Dynamics Simulations of a DNA Dodecamer Using AMBER 4.1 and Particle-Mesh Ewald Method

Abstract

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.