Practical Four: Molecular Dynamics

(1) Methylcyclohexane ring flipping

Calculate structure of methylcyclohexane, using AMBER and implicit hydrogens. This will allow the computer to calculate the energy quickly. After minimisation, set up a molecular dynamics run. Click on DYNMCS, then MDyn. Choose automatic set up, which will set up a 10 ps simulation at 300 K. Click on Start to begin the simulation. How do the structure and energy change as the simulation proceeds? Does the ring flip from equatorial to axial? Try the simulation again, beginning with axial methylcyclohexane. Do the molecules behave as you would have predicted?

(2) Hydroxyketone dynamics

Minimise this hydroxyketone using MacroModel, the AMBER force field, and explicit hydrogen atoms. The global minimum structure has a hydrogen bond between the alcohol and the ketone. Manipulate the structure so that this hydrogen bond is present using Rot T to alter torsion angles.

Set up a 10 ps molecular dynamics run on this structure (AMBER, explicit hydrogens, 300ÊK), leaving the atomic distance highlighted, so you can monitor it as the run proceeds. Note the maximum and minimum distance between the hydroxyl hydrogen and the carbonyl oxygen.

Repeat this, but now with the solvent model for water turned on. Does it make a difference to the molecule?

(3) DNA dynamics

A molecular dynamics simulation on DNA takes some time to calculate. A movie of the result of such a simulation is in the directory /usr/local/examples. Copy the files to your local directory by typing 'cp /usr/local/examples/DNA.* .' into a UNIX window, then watch the movie by going to the ANLYZ mode of MacroModel, and clicking on the Movie button. Don't forget to delete the files again when you have looked at them! (Type 'rm DNA.*')

An example of DNA dynamics may be viewed over the WWW, provided you browser supports multiframe gif images - try it and see!