Problem with Ligand COM drift and RMSD graphs (png)

[BillSwope]

Graphs (png files) produced at the end of a simulation showing LIgand COM drift and Ligand RMSD do not appear to have treated PBC correctly. If we look at the trajectory file produced, there is almost no movement of the ligand relative to the protein. However, the graphs suggest movement by 100 Angstroms. This was observed with OpenFE v 1.7.0.

To Reproduce
Steps to reproduce the behavior (ideally a minimally reproducible example):

Software versions

• Which operating system and version did you use? (e.g. ubuntu 22.04.5)Linux
• Which method did you use to install this package? (e.g. conda-forge)
• Copy/paste the output of conda list (or the equivalent for your package manager):

Output

Expected behavior

Additional context

[IAlibay]

Thanks for reporting this @BillSwope !
We were aware of periodicity issues with protein RMSD, this might be a new one for us to look into.
By any chance, is your system containing multiple chains?

[BillSwope]

As a matter of fact, THREE chains. It's a GABA protein with about 16K atoms.

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On Mon, Feb 9, 2026 at 1:40 PM Irfan Alibay ***@***.***> wrote: *IAlibay* left a comment (OpenFreeEnergy/openfe#1834) <#1834 (comment)> Thanks for reporting this @BillSwope <https://github.com/BillSwope> ! We were aware of periodicity issues with protein RMSD, this might be a new one for us to look into. By any chance, is your system containing multiple chains? — Reply to this email directly, view it on GitHub <#1834 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ARBVQIEBTL5R2MRF6D7EPS34LD5EPAVCNFSM6AAAAACUQ6XTGOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTQNZUGAYDQNZVGY> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[BillSwope]

Irfan, I checked a different protein, with only one chain (CDK8), and with my OpenFE v1.4 the Ligand RMSD and drift graphs look fine. Regards....Bill

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On Mon, Feb 9, 2026 at 2:25 PM William Swope ***@***.***> wrote: As a matter of fact, THREE chains. It's a GABA protein with about 16K atoms. On Mon, Feb 9, 2026 at 1:40 PM Irfan Alibay ***@***.***> wrote: > *IAlibay* left a comment (OpenFreeEnergy/openfe#1834) > <#1834 (comment)> > > Thanks for reporting this @BillSwope <https://github.com/BillSwope> ! > We were aware of periodicity issues with protein RMSD, this might be a > new one for us to look into. > By any chance, is your system containing multiple chains? > > — > Reply to this email directly, view it on GitHub > <#1834 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/ARBVQIEBTL5R2MRF6D7EPS34LD5EPAVCNFSM6AAAAACUQ6XTGOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTQNZUGAYDQNZVGY> > . > You are receiving this because you were mentioned.Message ID: > ***@***.***> >

[IAlibay]

Thanks @BillSwope - this is useful info, it might be the same thing Hannah is already in the process of fixing in openfe-analysis (hopefully!)

[BillSwope]

More facts about the bug. I have been messaging my colleague at Genentech who has also seen this problem. She said she has a system with only one chain, and the graphs were good from OpenFE 1.6, but not from OpenFE 1.8. So, it might not be related to just the number of chains. I hope this is useful....Bill

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On Mon, Feb 9, 2026 at 2:52 PM Irfan Alibay ***@***.***> wrote: *IAlibay* left a comment (OpenFreeEnergy/openfe#1834) <#1834 (comment)> Thanks @BillSwope <https://github.com/BillSwope> - this is useful info, it might be the same thing Hannah is already in the process of fixing in openfe-analysis (hopefully!) — Reply to this email directly, view it on GitHub <#1834 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ARBVQIECM66UL2XS6OPMB334LEFRBAVCNFSM6AAAAACUQ6XTGOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTQNZUGI4DMMJXGM> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[IAlibay]

Ah, that's very useful! Sounds like the dodecahedron box might be the culprit.