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We have found a problem in pymbar/examples/alchemical-free-energy/parsers/parser_gromacs.py with parsing large dhdl.xvg files. In slice_data(), there's a line:
f.len_first, f.len_last = (len(line.sp…
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This comment is for @mrshirts and @jchodera with relation to the implementation and theory in `fes.py` for samples
I managed to accidentally recreate the bug in #502 and have attached a minimal scr…
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Moving from the general task #255 to specific tasks
- [x] Decide what to do about deprecation for old names and results structures. Do we just support the new ones? Do we add specific errors for …
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We probably want a scheme to automatically discard initial BHMM samples to burn-in. One way to do this would be to record the log-likelihood of the BHMM posterior and then use [automated equilibratio…
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You should take the fraction_contacts_expectation function in secondary_structure.py as the example. Instead of passing in a native contact list and a distance cutoff, you pass in a general function …
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I am running temperature replica exchange simulations on small coarse-grained oligomer systems (containing a single chain), and have been using an ensemble validation check on the energies for thermod…
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Hey guys,
I was recommended to post this issue here by @jchodera.
I've been trying to use openmmtools' alchemy.py code to compute solvation free energies of an ethanol molecule in water. The mai…
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Looks like from my runs last night that this is _very_ slow on the whole dataset. I'll profile and figure out what could possibly be done (possibly parallelize the reweighting step?). Not sure what pr…
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In line with the overall [API proposal](http://alchemlyb.readthedocs.io/en/latest/api_proposal.html), we want to have parsers for each of the major MD engines, and eventually have coverage for all of …
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What is the best way for us to ensure reproducibility by making older releases available in perpetuity?
Keeping packages only on binstar is not necessarily safe; we may want to archive older release …