QM/MM calculations on thymine dimer repair.
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 |
updated 28/10/08