[General]: CodeEntropy fails for gas-phase MD simulations without periodic boundary conditions (PBC) #446

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1. harryswift01 commented on Oct 9, 2026

   

   harryswift01

   on Oct 9, 2026

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   Hi CodeEntropy developers,

   I am trying to use CodeEntropy to calculate configurational entropy for a small molecule simulated using molecular dynamics (MD) in the gas phase with AMBER. Since this is a gas-phase simulation, I am not using periodic boundary conditions (PBC).

   However, CodeEntropy fails during the initial trajectory processing with the following error:

   AttributeError: 'NoneType' object has no attribute 'copy'

   The traceback points to CodeEntropy/trajectory/mda.py, inside the merge_forces() method, where the code attempts to extract trajectory dimensions:

   dimensions = self._extract_timeseries( select_atom, kind="dimensions" )

   Within _extract_timeseries(), the code attempts to execute:

   values.append(universe.dimensions.copy())

   For a non-periodic gas-phase trajectory, universe.dimensions is None, so this operation raises an AttributeError.

   Additional Information

   I would expect CodeEntropy to support non-periodic trajectories. Gas-phase MD simulations of isolated small molecules are a useful application, particularly for calculating molecular configurational entropy and investigating its relationship with properties such as solubility.

   Hi @HafizSaqibAli, thanks for bringing this to our attention. I am happy to take a look into this for you now.
2. harryswift01

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   on Oct 9, 2026
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   added this to the 2.5.0 milestone on Oct 9, 2026
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   linked a pull request that will close this issueSupport non-periodic trajectories without box dimensions #447on Oct 9, 2026
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   closed this as completedin #447on Oct 9, 2026
8. harryswift01 commented on Oct 9, 2026

   

   harryswift01

   on Oct 9, 2026

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   Hi @HafizSaqibAli , thanks again for bringing this to our attention. We have now shipped a new release of CodeEntropy, v2.5.0, which allows calculations on trajectories with no PBC. We tested it on your gas-phase system and it now runs without the AttributeError.

   You can update with either:

   pip install --upgrade CodeEntropy
   

   or

   conda install -c conda-forge -c ccpbiosim codeentropy=2.5.0
   

   Please let us know if you run into anything else. I'll close this issue for now, and feel free to reopen it if needed.