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OpenMM 8.1 has a performance improvement for larger systems: https://github.com/openmm/openmm/pull/4147.
I attempted to port it myself but was unsuccessful. [findInteractingBlocks.hip](https://gith…
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Hi There,
I first want to say that for my cases PDBFixer is superior to other methods. For the case of 7zaw.pdb - Human GPC3 having missing atoms and residues (many) - PDBFixer is able to add the m…
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As in https://github.com/openmm/openmm-torch/issues/33, I am trying to implement a SchNet neural network into OpenMM for md simulations. I wrote the ForceModule as in https://github.com/openmm/openmm-…
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Hi,
I am trying to install openMM on MacOS Mojave and I keep getting error messages, the last one included that the python I have on my computer is not suitable. Any idea how can I fix that?
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I'm experiencing some slow downs in performance when using the NetCDF reporter from MDTraj versus the DCD reporter from OpenMM.
When using the NetCDF reporter the performance declines the longer th…
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Hi!
I'm experiencing troubles when running MD simulations on metalloprotein (LmrR, 139k atoms in system) with OMMprotocol. So I keep randomly getting this CUDA error (700) and due to this sometimes…
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Our recent [OpenMM 7.6 release](https://github.com/openmm/openmm/releases/tag/7.6.0) included some namespace changes that look liked they required pinning this repo to OpenMM 7.5.1.
Is it OK with y…
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Often, I want to save structures of molecules from a simulation (i.e. gas phase) to a format which retains the charges, bond orders, and coordinates. None of the current `OpenMM` reporters can retain …
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Hi,
I am
![1_gromacs_ff](https://cloud.githubusercontent.com/assets/21062948/25709419/98b399f8-30e9-11e7-8979-c4e5bec404d9.png)
![2_openmm_ff](https://cloud.githubusercontent.com/assets/21062948…
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notebook link: https://colab.research.google.com/github/KULL-Centre/papers/blob/main/2022/ML-ddG-Blaabjerg-et-al/RaSPLab.ipynb
Error message:
```python
During handling of the above exception, anoth…