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It just came to my attention that OpenMM 7.4.0 is made available as a debian package maintained by @merkys via https://salsa.debian.org/merkys-guest/openmm
See https://lists.debian.org/debian-devel…
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Description:
When parameterizing water model using Liquid targets, OpenMM engine gives error when loading `liquid.pdb`:
```ValueError: Residue 4 (HOH) does not match any template defined by the Forc…
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Would it be possible to provide OpenMM builds for Python 3.8? Current OpenMM Conda builds are for Python 3.7. Python 3.8 was released about 1 year ago, and python 3.9 is about to be released (first …
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Hi,
I am trying to get a plugin working that is only compatible with Openmm < 8.0 (mainly due to removal of fftpack.h), and currently using Openmm 7.7. The install seems all working well, but in Py…
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## Expected behavior ##
I have a workflow where I'd like to be able to feed in my PDB topology and DCD trajectory data from streams. The [Universe](https://docs.mdanalysis.org/2.5.0/documentation_p…
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## Motivation
Membrane-protein systems account for ~ 60% of possible target space. Being able to calculate binding free energies for membrane-containing systems would be a significant advantage.
…
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## Expected behavior ##
Hello,
I am using MDAnalysis to compute PCA on a big set of pdb file.
```
u = mda.Universe(files[0], files)
```
## Actual behavior ##
When I have more than rou…
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Would there be an available Jupyter notebook for the ESMACS protocol (using OpenMM) that covers the set-up (including parametrization) until analysis and obtaining the binding free energy?
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A recent restructuring of the OpenMM section of nanover-protocol means that the python server behaves more like the rust server (in that the data from the simulation is retrieved via .getState rather …
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Ambertools 23 had a behavior change https://github.com/openmm/openmmforcefields/issues/281 from ambertools 22 that is causing some issues downstream. If we had an ambertools 22 build for python 3.11 (…