Repository navigation
[General]: CodeEntropy fails for gas-phase MD simulations without periodic boundary conditions (PBC) #446
Description
Activity
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.
- linked a pull request that will close this issueSupport non-periodic trajectories without box dimensions #447
on Oct 9, 2026 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 theAttributeError.You can update with either:
pip install --upgrade CodeEntropyor
conda install -c conda-forge -c ccpbiosim codeentropy=2.5.0Please let us know if you run into anything else. I'll close this issue for now, and feel free to reopen it if needed.
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.