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Parallel bias metadynamics #131

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@sivadasetty sivadasetty commented May 12, 2022

Implementation of Parallel Bias Well-tempered Metadynamics (PBMetaD) as described in Pfaendtner and Bonomi, J. Chem. Theory Comput. 11, 5062–5067 (2015).

  • Added optional support for grids.
  • Added analysis module to obtain free energy along each CV.
  • Added example Python script of ADP system to estimate free energy along $\phi$ and $\psi$.

adp-fe-dyn-2

@sivadasetty sivadasetty marked this pull request as draft May 12, 2022 14:00
@sivadasetty sivadasetty changed the title Parallel-bias metadynamics Parallel bias metadynamics May 12, 2022
sivadasetty and others added 25 commits July 18, 2022 15:29
@sivadasetty sivadasetty marked this pull request as ready for review July 31, 2022 04:24
@sivadasetty sivadasetty marked this pull request as draft July 31, 2022 04:58
@sivadasetty sivadasetty marked this pull request as ready for review July 31, 2022 05:24
@sivadasetty sivadasetty marked this pull request as draft July 31, 2022 05:25
@sivadasetty sivadasetty marked this pull request as ready for review July 31, 2022 05:51
should_deposit = jit(lambda pred, _: pred)

else:
grid_mesh = compute_mesh(grid) * (grid.size / 2)
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grid_mesh variable should have the same value as in metad.py line 236:
grid_mesh = (compute_mesh(grid) + 1) * (grid.size / 2) + grid.lower

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3 participants