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```
I think there is a bug in the SireOpenMM free energy single topology code. The problem is that 1,5 or greater pair-pair interactions in the same solute are computed using a reaction field …
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Let's be sure what we're asking in the modelling, before we submit a request to e.g. Bun to resolve these matters. My first shot is below. Are these the interesting questions? Are these the relevant m…
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Hi,
Forgive me if this is elementary. I want to compute reaction rates between an open and closed ring in a molecule.
If we take a z-matrix of the input and output
And pass it throug…
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Hi,
I'm using GIST to measure energetics of water displacement upon ligand binding to a protein cavity. I've been following this [tutorial from ambermd.org](https://ambermd.org/tutorials/advanced/tu…
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Great paper! Here are a few items for your consideration...
page 20, 5 lines above section 7: practise-->practice
page 22, second bullet: cyro-->cryo
page 22, first bullet in Affinity data ("…
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```
I think there is a bug in the SireOpenMM free energy single topology code. The problem is that 1,5 or greater pair-pair interactions in the same solute are computed using a reaction field …
-
### Problem
At the moment, all analysis in pourbaix_diagram.py assumes that we are operating under room temperature. As a result, we assume all free energies will have a prefactor of 0.0591 for the…
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We should look into why calculations spend so much time writing sampler states, and why this time increases with iteration number.
Some thoughts:
* We very likely should not be calling `sync()` ev…
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The parameters of the free energy depent on the values of the surface $\gamma_s$ and grain boundary $\gamma_{gb}$ energies and the diffuse interface thickness $\delta$ as follows:
```math
\begin{ali…
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For certain types of overlapping distributions, the uncertainty estimate returned by BAR can be`nan`
``` python
%matplotlib inline
import numpy as np
import pymbar
from matplotlib import pyplot…