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Hi,
I am running NVT equilibration and the following error is raised:
openmm.OpenMMException: Particle coordinate is NaN.
My system has been minimised properly with the potential energy conve…
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The `addSolvent` method uses a force field to assign charges, which it then uses to add ions that neutralise the net charge of the box. Unfortunately, the force field seems to assign formal charges of…
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This is a meta-issue to serve as a list of the different integrations between metatensor atomistic models and simulation engines. Any longer discussion should be split into a separate issue and linked…
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When I run my script, i got some strange error:
```
/home/coder/miniconda3/envs/htmd_env/lib/python3.7/site-packages/simtk/openmm/app/charmmparameterset.py:389: UserWarning: Replacing dihedral with…
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Reported for nanotube in SubtleGame
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On the third code cell, the following warning appears
```
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
/home/michael/.miniconda3/envs/teachopencadd/lib/python3.9/site-…
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When I try to fix a protein (PDB ID: 2xgc), the exception is:
```
Traceback (most recent call last):
File "/home/huang/project/deepkaserver/model/deepka/deepka.py", line 56, in preprocess
fi…
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OpenMM's Modeller uses a neutralize-then-add approach, which probably yields different values: https://github.com/openmm/openmm/blob/master/wrappers/python/simtk/openmm/app/modeller.py
It should be…
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Thanks for the amazing tutorial! It is very helpful!
I wonder why in most OpenMM protocols the temperature is directly set to the production temperature? In comparison, most Amber tutorials have an…
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Now that we have a CI workflow working with CGOpenMM, we need to come up with some tests for the CI to run.