Free Energy Purturbation and Hamiltonian Replica Exchange
Is there a way to introduce a coupling parameter to a solute in order to run Free Energy Perturbation or Hamiltonian Replica Exchange for solvation free energy or binding free energy calculations? I don't believe Abalone is currently set up for this, but I was wondering if there would be some way to run the calculations anyway?
If not, can you recommend some ofter method for determining binding and solvation free energies?
Thanks for the continual support. This is a wonderful simulations package.
Re: Free Energy Purturbation and Hamiltonian Replica Exchange
Thanks for the tip. I will certainly give this a try. In the mean time, I'm trying to perform calculations in the NPT (isothermal/Isobaric) ensemble. I'm currently thermally relaxing my system using the Berendsen thermostat, and performing my production runs using:
Berendsen Borostat (pressure set to achieve desired average density)
Velocity Verlet Integration @ 1fs MD step