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Trying to enumerate all the ways that perses can be used, and might be used in future
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Perhaps I should reopen an issue and describe it [here](https://github.com/Gallicchio-Lab/AToM-OpenMM/issues/21#issuecomment-2212364700).
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There are various free energy methods that utilize scaling of intermolecular interactions. For example one can compute the chemical potential by inserting an additional particle/molecule into the syst…
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### Describe the Bug/Issue
Hello,
I'm debugging why my mac won't go to sleep, and the last app that is showing up for me as "Preventing Sleep" in activity monitor, is cursr:
### Steps to Reprod…
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Hello All,
I'm building a project based on `embedded-hal` and `embassy` for various boards that does async operations.
When doing research I noticed that the `embassy-rp` crate doesn't expose the…
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Over the past few months, I've been navigating through some challenging personal circumstances that have significantly limited my availability. Alongside these personal matters, my schedule has become…
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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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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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It would be nice to add a few test systems here:
- two Lennard-Jones particles with and without opposite charges
- two water molecules
- an artificial binding site made of Lennard-Jones atoms
- one wa…
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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…