What is TMB‐IBIOMES

Louisiana Tech’s Theoretical Molecular Biology Lab’s iBIOMES Lite database presents over 20 microseconds of all atom molecular dynamics simulations for over 500 different realizations of the nucleosome. For... every simulation the following files are presented: initial Amber formatted parameter and topology files (*.parm) and coordinate files (*.crd) with and without solvent (sys.* and nowat.*, respectively). namd2 formatted configuration (*.conf) and output files (*.log), dewatered DCD trajectory files (*.dcd), RMSD trajectory data (*.png and *.dat), and inter and intra basepair stacking and step parameters (*.nastruct.dat). Closely related simulations are grouped together and a summary of DNA helical parameter data and Cartesian coordinate RMSD data is provided. All of this data can be navigated in a file browser format or downloaded directly with command line tools or accessed via an iBIOMES Lite instance.