QM/MM tutorial


QM/MM calculations on thymine dimer repair.


VII. The effect of electron uptake II, enhanced sampling with chemical flooding

QM/MM MD with a flooding potential

We apply the flooding potential in all collective degrees of freedom and continue the QM/MM simulation. We use the last frame of the previous QM/MM simulation as a starting structure for the flooding run:

grompp -f qmmm2.mdp -p qmmm.top -n qmmm.ndx -c qmmm2out.gro

./mdrun -v -c qmmm3out.gro -ei sam.edi -x traj_VII.xtc

Again, since the run will take up to 40 minutes, we have made the output available for you to download: electron2.tar.

The last frame of the flooding simulation is shown in Figure 5. We see that both covalent bonds between the bases are broken. However, there is still an excess electron on one of the bases, which is reflected by the sp3 hybridization of the pyrimidine nitrogen atom.

Figure 5. With the flooding potential the thymine dimer is completely broken within 2 ps.

In reality, the electron is transferred back, either to the FADH cofactor in Photolyase, or to an adjacent base in the DNA strand. To account for this back-transfer in our simulation, we continue the simulation from the last frame, using the old mdp file for the neutral singlet QM subsystem.

grompp -f qmmm1.mdp -p qmmm.top -n qmmm.ndx -c qmmm3out.gro

./mdrun -v -c qmmm4out.gro

The output files are available here: final.tar.

The last frame of the simulation is shown in Figure 6. We see that the DNA is completely restored!

Figure 6. Restored DNA.

Next:VIII. Concluding remarks
Previous: VI. Setting up Chemical Flooding

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updated 28/10/08