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Hi, I run example of yank, run-explicit.sh, and meet the error as follow, and my Yank Version is 0.25.2. mbar is 3.0.5.dev-Unknown, openmm is 7.6.0.dev-ad113a0.
dcdplugin) Could not access file 'ex…
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@mrshirts @jpotoff @msoroush
> On page 5 in the third paragraph the authors admit that GCMC-MBAR is very similar to HS-GCMC in nature. They are both powerful tools to optimize force field paramete…
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Here is an example that came up in a discussion with @mrshirts , where MBAR's uncertainty estimate can revert to a small number when the overlap is brought close to 0.
For comparison, naive impleme…
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Repro steps:
1. Enter the following: `foo ^Gbar`. Should display as `foo ^Mbar`.
2. Copy it to clipboard with `yy`
3. Paste it with `p`
4. Should paste properly as `foo ^Mbar`
5. Try it with s…
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- [ ] Include bootstrapped uncertainties from MBAR:
- [ ] When comparing MBAR and HR
- [ ] When plotting the optimal epsilon-scaling factor
- [ ] Analyze generalized Potoff and TraPPE fo…
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Unit conversions sometimes convert Float32 to Float64
```julia
julia> uconvert(u"°C", 1.0f0 * u"°F")
-17.222198f0 °C # stay in Floa32
julia> uconvert(u"mbar", 1.0f0 * u"psi")
68.94757293168…
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We need to accelerate the inner loops.
I think the most important things to do would be to accelerate in this order
* logsumexp.
This is the largest cost.
After that is accelerated, it'…
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### Windows build number:
Microsoft Windows [Version 10.0.22000.1455]
### Your Distribution version:
Debian Release: 10
### Your WSL versions:
C:\Projects\vplk\PerlVPClient>wsl --version
…
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I tried the alchemical free energy calculation example for a Lennard Jones fluid (http://openmm.org/tutorials/alchemical-free-energy/) and it crashes with mbar having issues with having non-1 sum for …
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The 3.0 API had a `method` argument to the `MBAR` that allowed the value `self-consistent-iteration`:
```python3
pymbar.MBAR(mU_kln, mN_k, ..., method='self-consistent-iteration')
```
I'm stru…