QM/MM calculations on thymine dimer repair.
QM/MM MD simulation
We now perform a short 1ps QM/MM (AM1/Amber99) equilibration simulation of the
system.
For this part, we need a special mdrun binary that has been linked with the mopac library. You can download this binary here mdrun.
To make the mdrun binary executable, use
chmod +x mdrun
We keep using the normal grompp version.
grompp -f qmmm1.mdp -p qmmm.top -n
qmmm.ndx -c qmmm1.gro
./mdrun -v -c
qmmm1out.gro -x traj_stepIV.xtc
Since this run will take approximately 40 minutes, we have provided the
outputfiles as a tar-file: qmmmmd.tar. You can
either use these files to proceed to the next step, or wait until your own run
is finished. Uncompress the file with
tar -xvf qmmmmd.tar
In the next step we will use the structure after 1 ps to investigate
the effect of an excess electron on the stability of the thymine
dimer.
| Next: | V. The effect of an electron uptake I | Previous: | III. Setting up the system for QM/MM simulation |
updated 28/10/08