QM/MM tutorial

QM/MM calculations on thymine dimer repair.

I. Equilibration of DNA with Gromacs

Classical Molecular Dynamics

We will perform a 1 ns classical molecular dynamics simulation of the system, consisting of a 20 basepair DNA molecule with a thyine dimer, water and ions. As a starting structure for the simulation we use the equilibrated structure from the building session.

localhost:~>grompp -f md.mdp -p neutral.top -c neutral_sol_equi.pdb -n neutral.ndx

localhost:~>mdrun -c equi.gro

Note that we now use the gro file-format, because we want to use not only the equilibrated coordinates, but also the velocities in the next step.

Next:III. Setting up the system for QM/MM simulation with gromacs
Previous: I. Building a model of a solvated double stranded DNA molecule with a dimer lesion

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updated 28/10/08