What is the TMB Library?

DOI: 10.1021/acs.jcim.9b00252

Bishop’s TMB library 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.