DNA kinks from biased MD simulations

The dataset contains the necessary information supporting the findings of the study titled “Inferring Kinkability from Biased MD Simulations.” It includes: 

PDB files generated using cgDNA+,

Scripts for running RBB-NA molecular dynamics simulations,

Python scripts for WHAM analysis and figure generation.

The folder figure_crystal_structure contains PDB files for visualizing crystal structures, analyses performed via 3DNA, and the corresponding results in PDF format.

The folder simulations includes two data_guide files that explain the contents and provide instructions for reproducing the simulations. NOTE: the file in the control folder used in GROMACS preparation step and simulation (mdp files) are not present here. We used mdp files provided in RBB-NA github repository, available via the paper titled "Rigid Base Biasing in Molecular Dynamics enables enhanced sampling of DNA Conformations", see the references of the dataset.

For additional data, including output files from RBB-NA simulations (XTC and TPR formats), please contact the dataset creators.