PDB2MD

Introduction

Here the PDB2MD engine has been used to run fully solvated MD simulations on a total of 96 different DNA sequences taken from the PDB/NDB. So far 1-2 ns of MD has been run on each sequence. This has consumed a total of about 1.8 CPU years and has generated approx. 40Gb of trajectory data.

The outline of the protocol used is as follows:
DNA solvated with TIP3P waters using truncated octahedral PBC and 12 angstrom cut-off. Systems neutralised by addition of potassium counterions. Standard multistep energy minimisation and restrained dynamics protocol used for equilibration. 1-2 ns of production NPT MD using Amber8 PMEMD, snapshots saved every 1 ps.

Basic analysis of the simulations includes PCA analysis to check for equilibration and sampling, and Curves analysis of helical parameters. Plots for the PCA analysis, two key helical parameters - average X-displacement and average twist, and dials plots for the backbone torsions are included below. Note that in the dials plots, small tick marks on the dial peripheries mark the crystal structure values.
The simulation data will be deposited and available via the BioSimGrid project.

Results