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We have found a problem in pymbar/examples/alchemical-free-energy/parsers/parser_gromacs.py with parsing large dhdl.xvg files. In slice_data(), there's a line:
f.len_first, f.len_last = (len(line.sp…
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I was trying to run the Alchemical free energy calculations example as is on a CPU and a gpu - both cases don't run to completion.
but the errors are different.
On the cpu I get
Minimizing energy…
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I think it's related with Brewing API as brewing stand found in village is vanilla stuff and for Alchemical Catalyst is Brewing API stuff required but it's not apparent in the Lexica Botania (but it's…
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I noticed that some people (for example: https://github.com/MobleyLab/alchemical-analysis/blob/37b21ebb6d0495990c43595d9ade10c779c3ab08/alchemical_analysis/alchemical_analysis.py#L650) just use the su…
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I have installed openmm, as well as run the simtk test, and it checkout out as okay.
Currently I am running the alchemical tutorial for a LJ system to get a feel for openmm. I have run into 2 issue…
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Dear Mobley lab,
I am trying to run the alchemical-analysis tool on a set of output files from Amber TI simulations. The tool successfully computes dG, but fails to compute BAR/MBAR results and out…
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As the title suggests, the Alchemical Boiler does not work with IE's External Heater.
I would normally post this on IE's github, but I believe this might be on Automagy's end since the External Hea…
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CC #848
Examine Alchemical forces into separate Force Group for `RestCapableHybridTopologyFactory`
The NonBonded force that handles env env interactions can be in its own force group.
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@pgrinaway has added a neat feature to `HybridTopologyAlchemicalFactory` that allows the user to specify a set of alchemical functions to the factory. These are used to define how `lambda_sterics` ,`l…
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Currently, the `alchemy` module uses [this code to identify controllable alchemical global parameters](https://github.com/choderalab/openmmtools/blob/321b998fc5977a1f8893e4ad5700b1b3aef6101c/openmmtoo…