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The documentation, in particular the one in Turing.jl itself, is in dire need of update given the amount of features and improvements we've made over the past year. In particular, the tutorials have l…
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There should be a way to get the final sorted list of actions to override which one gets picked.
Maybe there is a need for randomization or maybe avoid babysitting score values for exceptions that c…
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Hi James,
Thank you for your lazymcmc package! I've been using it to fit an SEIR model. I can run one chain, no problems, but when I parallelise using foreach, an extra parameter appears in the out…
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In section 8.3, many estimators were summarized. Is it possible to also have some description on WHAM? Because WHAM was mentioned a few times in the paper (especially in the "recommendations"). Thanks…
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[prior-srcmchirp]
name = external_func_fromfile
module = pycbc.distributions.external
file_path = /home/QiYanQing/GWTC_reweight/Bayesian_inference_20230203/CE/GW190421_213856/prob_chirp_mass_source…
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I've been working with the replica exchange module, trying to run standard temperature REMD. I set up an OpenMM script using the proposed format here: [openmmtools--Missing feature for Replica Exchang…
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@dominicrufa and I were trying to run repex on the endstates of a capped amino acid transformation (ALA->THR) (using the new [RepartitionedHybridTopologyFactory in perses](https://github.com/choderal…
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When using parallel tempering, the chains are instantiated by a single thread. When the likelihood is numerically unstable, it can take many retries to get a good initial parameter set. Spread across …
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My colleges and I currently use LAMMPs to generate new data within our workflows. The main advantage is the flexibility and performance of LAMMPs compared to ASE. Thus I thought it would be nice to ha…
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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…