Free Energy Perturbation Modules

Free energy perturbation methods can be used to determine solvation energies and energies for changes in structure or ligation of biomolecules. These methods are related to statistical mechanical perturbation theory methods.

The classic example of a free energy perturbation is the comparison of the solvation energy of ethane and methanol shown below.

Figure 1. Ethane in aqueous solvent.

The parameters for ethane are mutated gradually to those of methanol shown below.

Figure 2. Methanol in aqueous solvent.

In order to carry out the free energy perturbation download the car, mdf and input files.

ethane_box.car

ethane_box.mdf

ethane_box.inp

Note that to carry out a free energy perturbation you must run DISCOVER2.9 not DISCOVER3.0 as we have done previously. Inspect the input file to note the different form. To lauch the job type

Ø discover

at the prompt. Then supply the necessary information. At the prompt for the filename type the root name. If you keep the same name as above this would be

Ø ethane_box

Use the cvff forcefield (selection 1 for the forcefield).

Use the default nice number (nice number = 19) so that the job will run in the background. Use 1 processor.