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Hi
I'm trying to run the T4 lysozyme example with p-xylene in yank. However, during the replica exchange simulation it is throwing an error which i am finding difficult to troubleshoot (see attache…
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**Description**
User case:
I construct an Interchange object from a Topology with two or more ismorphic Molecules with different partial charges.
In this case the first Molecule has am1bcc char…
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It's useful for S-S bond to guide tleap.
What do you think?
```python
bonds = [(10, 20), (100, 200)] # List of atom pairs
parm.write_pdb(...., conect=bonds)
```
Note: not write all 'CONECT'…
hainm updated
2 years ago
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Cannot find packmol.exe in the zip file.
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Hello,
I've been trying to simulate custom liquid systems using BAMBOO. After installation, the demo system runs well with the provided demo data in benchmark subdirectory.
I'm wondering whether…
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Trying to use the pre-trained espaloma-0.3.0 on my supercell, and came across this vague error that I can't seem to get the origin of?
```
/home/hy2120/miniconda/envs/openff/lib/python3.10/site-pa…
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The `from_pandas` method of the `openff.evaluator.datasets.PhysicalPropertyDataSet` object returns an instance of the `PhysicalPropertyDataSet` object, but the `from_json` method returns a dictionary.…
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I'm trying to partially reproduce the setup here, probably only to generate the condensed phase systems, and I'm having issues creating the conda environment that should be made generally known:
``…
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I'm opening this issue to perhaps provide some information concerning the discussion that we might have on Jul 7.
I've tested quickly here the computation of a nb list with `NeighbourLists` and `C…
lmiq updated
5 months ago