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Hi,
I have already executed simulations for my membrane protein complexes, I have over 30 complexes. I have executed relative binding affinities and now want to execute absolute binding free energy c…
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When running this prospectively, I just use random numbers in the experimental block, but is there an easier/tidier way to get the per-node (relative)absolute free energies from a set of relative free…
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Currently we only support relative free energy calculations but absolute solvation free energy calculations are routinely carried out in the field with well described protocols.
@lohedges @ppxasjs…
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I'm experiencing some issues when trying to generate an `FEMap` with some computed DDGs and an absolute experimental DG for the reference compound. An example notebook that shows this is in https://gi…
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The statistical error is 40.48 while the bootstrap error is 0.35
The code to reproduce
```
import pymbar
import numpy as np
u_nk = np.load("u_nk.npy")
N_k = [10000] * 12
mbar = pymbar.MBA…
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When we refactor the relative alchemical factory to move it to `openmmtools`, we should consider allowing multiple alchemical regions to enable A->B and B->A transformations to happen with the same si…
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We can simplify the relative free energy calculation driver app if we have the alchemical factory "bake" the switching functions into the system so that we only need to drive `lambda` in the integrato…
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Hi!
V3's wake loss algorithm assumes that each turbine at a wind farm is capable of producing the same amount of power as the free stream wind turbines. As you note, that assumption breaks down in …
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**In broad terms, what are you trying to do?**
The [Diamond Light Source XChem facility provides a fragment screening service](https://www.diamond.ac.uk/Instruments/Mx/Fragment-Screening.html) for …
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I want to try to simplify the way standard state corrections are incorporated in Yank, and was hoping to get suggestions from @luirink and @davidlmobley.
For generality, Yank uses the concept of "pha…