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[WIP] Simple MM-GBSA implementation #22

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[WIP] Simple MM-GBSA implementation #22

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jchodera
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@jchodera jchodera commented Feb 14, 2019 •
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Description

This PR provides a simple MM-PBSA-like implementation that computes the difference in enthalpy between complex and protein+ligand using OpenMM for PME, RF, or GBSA simulations.

Todos

Notable points that this PR has either accomplished or will accomplish.

  • autodetect explicit or implicit solvent
  • create command-line driver with entry point
  • allow user to specify PME, RF, or GBSA simulations via CLI
  • allow user to specify convergence tolerance and maximum number of iterations or wall-clock time
  • make sure to clean up contexts
  • add unit tests and example input

@dww100 dww100 changed the title [WIP] Simple MM-PBSA implementation [WIP] Simple MM-GBSA implementation Apr 23, 2019
@jaimergp jaimergp mentioned this pull request Dec 5, 2019
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@jchodera @dww100