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@rmcgibbo @peastman: If this is no longer being actively developed, what would you think about moving this to the http://github.com/openmm org, with the hope that we could eventually get developer res…
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We should be able to stop and start simulations to use short queue-times rather than having to schedule enough time to
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Hi @DaniBodor @DarioMarzella
Following our discussion the other day, here is PDB that gives an error with the cysteine. I haven't inspected thoroughly to trace the source of the error.
```
· r…
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Hi @peastman.
I was thinking of making a pair-energy reporter for OpenMM which computes and stores the pair-energy histogram between a solute and the solvent during the simulation.
However, I wanted…
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I was trying to run the example protein of the documentation:
[ examples/input.pdb](https://github.com/openmm/openmm/blob/master/examples/input.pdb)
This was the code: [DOCUMENTATION CODE](http:/…
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When I install [https://github.com/openmm/openmmexampleplugin?tab=readme-ov-file](url),
After I downloaded and unzipped the file, I renamed it openmm, and then ran the commands in sequence
`
$ cd …
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(Forgive me if I am posting this in the wrong forum.) I am using openmm in a container built on [continuumio/miniconda3:4.9.2](https://hub.docker.com/layers/continuumio/miniconda3/4.9.2/images/sha256-…
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I wanted to point out a few things:
1. OpenMM has a python `Topology` object that looks fairly similar to your `Molecule` object, which might be helpful for interconversion
2. OpenMM has python-base…
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I have come across an error that is really perplexing me.
I have tried to create a custom integrator. It compiles, and tests are all successful. But when I come to make the python wrappers i run in…
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Hi,
I encountered a strange issue when using OpenMM + Plumed for an umbrella simulation between a protein and a DNA. I used the plumed to add a distance bias. But no matter which (groups of) atoms …