Flexibilize MM-GBSA calculation Part 1: Simulation.

[diegoenry]

There are multiple flavors for MM-(GB)SA, one should be abble to access at least some of the parameters within ScoreFlow during simulation.

1. Choice of simulation engine:
   AMBER serial: sander or pmemd ($$$)
   AMBER parallel: sander.MPI or pmemd.MPI ($$$)
   AMBER GPU: pmemd.cuda ($$$)
   GROMACS: gmx mdrun (free)
   GROMACS: gmx_mpi mdrun (free)

2. Choise of solvation model
   implicit: igb=2,5,8 for GBSA, igb=1,3 for PBSA.
   explicit solvent: Water model and box-size, counter ions must be added.

3. Simulation options.
   3.1) Minimization, number of steps (nsteps).
   3.2) Minimization (nsteps) + MD (nsteps)

MD must include a heating and equilibration protocol, followed by production