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Flexibilize MM-GBSA calculation Part 1: Simulation. #41

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diegoenry opened this issue Jul 12, 2018 · 0 comments
Open

Flexibilize MM-GBSA calculation Part 1: Simulation. #41

diegoenry opened this issue Jul 12, 2018 · 0 comments
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@diegoenry @donadef
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ScoreFlow Project

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@diegoenry
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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
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@diegoenry @donadef