Script and MDP files to perform molecular dynamic simulation of a protein-DNA complex in water box using GROMACS v.2019.
Content: amber99sb_bsc1mod.ff.zip (Compressed directory with Force field files from Amber-99SB-ff with bsc1-ff modifications for nucleic acids); ions.mdp, em_prot-dna.mdp, nvt_prot-dna.mdp, npt_prot_dna.mdp, md_prot-dna.mdp (GROMACS Molecular Dynamic Parameters files); md_prot-DNA.sh (shell script with MD step by step command line).
Protein-DNA trajectory movie: https://youtu.be/F6c-wVX49TQ
Gromacs tutorials for protein, protein-ligand and others: http://www.mdtutorials.com/gmx/