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For alchemical intermediates, a smaller cutoff can be selected provided good overlap is maintained.
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Up to this point we have used `lambda_electrostatics` to control the interactions rather than the charges, but if we want to keep things consistent we need to address these cases:
- With exact treatm…
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Exact ProjectE version: PE1.0.3B
Exact Forge version: 31.1.35
Steps to reproduce: Open Alchemical Bag with Quark mod installed.
When Quark is installed its inventory buttons overlay some slot…
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Hi All,
I have compiled alchemical_analysis/pymbar with python_2.7.9 and I could not export the overlap matrix within MBAR procedure, though MBAR free energy estimation worked well.
I got this …
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I've just crashed out my game by equipping an alchemical stasis ring while under the effects of regen 4 and I have no idea what to do to fix it >.<
https://gist.github.com/MuteTiefling/bd5b1aa363f…
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Just a heads-up that the relative alchemical factory here probably has the same issue we have in `AbsoluteAlchemicalFactory` where we neglected to add virtual site support:
https://github.com/chodera…
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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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From @peastman:
> Rather than using global parameters for the constants, I suggest hardcoding them in the expression. That is, add softcore_alpha=0.5; softcore_a=1; softcore_b=1; softcore_c=6 to your…
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There are a few minor things we should clean up for `alchemy.AbsoluteAlchemicalFactory`:
* The docs end up misformatting the context parameters
![image](https://user-images.githubusercontent.com/365…
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**Alchemist**: mage kit. Transmutation specialist. Can create unique alchemical items and can gain 7 ranks in alch. Penalty?