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Hi! After running openfold according to the default configuration, I found that there was a big difference between the output pdb file of openfold and alphafold (colab version). After comparing the re…
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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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I've been using OpenMM 7.7.0 and OpenMM-Torch 0.8 successfully to run a PyTorch model, however, when I add an RMSD biasing force to the system as well as the TorchForce, I get a segmentation fault upo…
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AMD GPUs seem to be getting more attention these days, and the HIP platform has much better performance than OpenCL. We should consider whether at some point we want to make it into a standard platfo…
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I am trying to locate the openmmtools functionality that corresponds to the 'DeviceIndex' property that can be passed to openmm's Simulation() to convey the available GPU devices. I am able to set the…
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Test this via OpenMM calculations of the density of pure solvents as Kyle Beauchamp did previously to verify we haven't done anything which messes this up. See under https://github.com/choderalab/Liqu…
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In pdbfixer 1.6, 1.7 and 1.8 and openmm 7.5.1 (and 7.6 running pdbfixer 1.8), The following line:
```python
fixer = PDBFixer(url=f'https://files.rcsb.org/download/{pdbid}.pdb')
```
fails with…
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- [x] I read [the conda-forge documentation](https://conda-forge.org/docs/user/introduction.html#how-can-i-install-packages-from-conda-forge) and could not find the solution for my problem there.
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I have defined a CustomNonbondedForce to calculate the non-bonding force between LIPF6 and EMC, but the original non-bonding force in the system needs to be deleted. I use nbforce.addException(i,j,0.0…
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As detailed in https://github.com/FoldingAtHome/openmm-core/issues/432 and https://github.com/FoldingAtHome/openmm-core/issues/364 the Centos6 EOL makes this image mostly unusable as you can't use yum…