Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations: Simulations Topology, Coordinate, Parameters, Input and Output files

The simulation data for the article: Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations.

ck_metad.tar.gz: Includes the topology files, coordinates files and gromacs parameter input file (.mdp) used for WT-MetaD-HREX simulations with different c(K+), which are newly added runs for resubmission. The corresponding script files and Plumed files are in GitHub.

eq_mini.tar.gz: Includes the parameter files required for the equilibration and minimization protocol.

standard_md.tar.gz: Includes the topology files and coordinate files for all systems built in the article. Also include the hbfix parameters file required on the MD run, and the MD script file.

metad.tar.gz: Includes the topology files, coordinates files and gromacs parameter input file (.mdp) used for WT-MetaD-HREX simulations. The corresponding script files and Plumed files are in GitHub.

metad*fe*.tar.gz: Plumed HILLS files and metad.bias data used for drawing the free energy landscapes.

ions.tar.gz: Data used for Figure.3 in the manuscript

si_data.tar.gz: All data used for SI figures.