Can we use molecular dynamics to simulate biomolecular recognition?

The starting structures (based on the crystal structure with PDB ID 1EFA), input files for GROMACS and PLUMED and scripts for prepartion and analysis are also available on GitHub. In this dataset, one can additionally find the trajetories of the simulations that were run to produce the linked publication.

The trajectories include the follwing sets: Unbiased simulations 5 replica of 50 ns each NMR restraint simulations 2 DNA sequences: specific, OSymL and non-specific NOD 3 replica of 250 ns each Metadynamics simulations OSymL (specific DNA sequence) bias on selected contacts between the protein and the DNA bias on selected contacts between the protein and the DNA and between the two hinge helices bias on selected contacts between the protein and the DNA and between the two hinge helices and the hinge helixity NOD (non-specific DNA sequence) bias on selected contacts between the protein and the DNA and between the two hinge helices and the hinge helixity Code contains the scripts used for preparing, running and analysing the simulations.