Open diegoenry opened 6 years ago
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 ($$$) GROMACS: gmx mdrun (free) GROMACS: gmx_mpi mdrun (free)
2) Choise of solvation model implicit: igb=2,5,8 for GBSA, igb=1,3 for PBSA. explicit solvent: Water model and box-size, counter ions must be added.
3) Simulation options. 3.1) Minimization, number of steps (nsteps). 3.2) Minimization (nsteps) + MD (nsteps)
MD must include a heating and equilibration protocol, followed by production
There are multiple flavors for MM-(GB)SA, one should be abble to access at least some of the parameters within ScoreFlow during simulation.
1) Choice of simulation engine: AMBER serial: sander or pmemd ($$$) 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