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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…
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When I run the FM1 tutorial example with the following execution:
```
(sire) spadavec@Crandall:~/itx/sire_example/ligandswap$ ligandswap -t0 rec_fmc.top -c0 fmc.30.crd -l0 FM1 -t1 rec_cti.top -c1…
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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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As was mentioned in issue #62, we need a way to validate or at least check the changes we make in SMIRNOFF.
When we changed `R` to `x` to get agreement between OpenEye SMARTS matching and RDKit re…
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**This is just a note/food for thought not a direct integration request**
I just came across this website by the EU, that allows to download EPW files for just about *ANYWHERE* in the world:
https…
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When taking the expectation of whether a structure is folded (1) or unfolded (0) on an mbar object, often the weights for folded state at high temperature are very small and negative (such as 1E-15 fo…
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Project Lead: @rgiessmann, @teddygroves
Mentor: @NPalopoli
***
Week 1: Meet your mentor!
- [x] Meet mentor for 30 minutes
- [x] Create an account on [GitHub](https://github.com)
- [x] Che…
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Trying python alchemical_analysis.py -d gromacs/data/3-methylindole-38steps -q xvg -p dhdl -u kJ -v
and I get
/usr/lib/python2.7/dist-packages/scipy/optimize/minpack.py:236: RuntimeWarning: xtol=0.0…
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In Gammapy we are making our first experiences with analyzing "real" exported DL3 data from IACTs. One problem we have seen in the past are noisy PSF histograms, which caused problems (especially at l…