Refactor RBFE code and fix various bugs #775
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proteneer
requested review from
maxentile,
mcwitt and
jkausrelay
and removed request for
maxentile
| all_fwd_delta_us.append(fwd_delta_u) | ||
| all_rev_delta_us.append(rev_delta_u) | ||
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| # sanity check - I don't think the dG calculation commutes with its components, so we have to re-estimate |
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@maxentile this is where the delta_U decomposition is done, I've added a comment here for future readers
timemachine/fe/rbfe.py
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| rev_delta_u = beta * (prev_U_fn(cur_frames, cur_boxes) - cur_U_fn(cur_frames, cur_boxes)) | ||
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| dG, dG_err = pymbar.BAR(fwd_delta_u, rev_delta_u) | ||
| dG /= beta |
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dg /= beta converts to kJ/mol (so update plot_BAR title units or convert after passing to plot_BAR)
timemachine/fe/rbfe.py
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| Configuration for the host system. | ||
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| n_frames: int | ||
| number of samples to generate for each lambda windows |
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"generate for endstate lambda windows"
Since you filter the intermediates below
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... where each sample is after 750 steps of MD.
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to clarify, this is saying that each window runs for n_frames*1000 steps of MD. It's independent of how many frames we store etc. I'll add a note in the return type that only first and last windows are currently returned.
WIP WIP WIP fat finger WIP WIP WIP labels Typing write less units label units Disable chiral terms in combine function Better schedule Oops Clean-up Add docstrings WIP Add more bins Update per jkaus comments Add a nightly test Improve plotting and address mcwiit and jfass comments Add matplotlib as a dependency
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lgtm! |
This PR
fe/rbfe.pyto be more modular