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Using the `MCMCMove.apply()` paradigm, I'm seeing this error. You can find my subclass `MCMCMove` [here](https://github.com/choderalab/perses/pull/396/files#diff-8c7c21f6a47e02cedcdc16233c702142R31), …
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This SAMPL, we are including a SAMPLing challenge, focused on looking at convergence of specific calculations with shared inputs (see #4 ). Right now we are focusing on host-guest binding prediction. …
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We need to figure out how we want to implement a storage and logging system for the initial command-line relative free energy application.
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Just opening an issue to record my experiments for reference.
With the current way we save strings, the `zlib` compression doesn't work. I was able to make it work by saving strings the old way as …
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For nearly the same experiment (only difference is slight change in `clearance` and existence of `switch_distance`), MC states seem to not mix in ```0.16```, while it seems to work in ```0.15``` (see …
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I have hybrid systems
[hybrid_fail.xml.zip](https://github.com/choderalab/openmmtools/files/1218966/hybrid_fail.xml.zip)
that work fine when they are used in a regular context creation, but on con…
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Hi,
After installing pymbar I tried to install the Alchemical Analysis package (https://github.com/MobleyLab/alchemical-analysis), but when I type "sudo python setup.py install" I get the error in th…
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Could you post some quick demonstration code on how to set up an OpenMM system using a specific value of the alchemical coupling parameter?
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Since all the relevant objects are initialized inside `Yank` (i.e. restraint, alchemical factory, sampling class), we need to pass all the parameters for all classes in a big `kwargs` dictionary. Then…
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I ran the same system with two different setups. In one, my 'receptor' is immersed in water using clearance = 16 A. In the other one I make my receptor periodic by setting the periodic box around it t…