Can we use molecular dynamics to simulate biomolecular recognition?

This Dataset contains starting structures, inout files and scripts to prepare and run normal and biased simulations on the LacI Transcriptionfactor and DNA (with different sequences). 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:
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<strong>Unbiased simulations </strong>
5 replica of 50 ns each
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<strong>NMR restraint simulations </strong>
2 DNA sequences: specific, OSymL and non-specific NOD
3 replica of 250 ns each
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<strong>Metadynamics simulations</strong>
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
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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
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Code contains the scripts used for preparing, running and analysing the simulations. It is also available on GitHub (https://github.com/mallu2/Transcriptionfactor_unbinding).