Set box size in Chemical system definition

[steinbt2]

The tutorials mention here: https://docs.openfree.energy/en/stable/tutorials/showcase_notebook.html in section 2.3 that one can provide box vectors to a Chemical System but I could not find a description how to do that. The Solventcomponent class also does not allow specifying a box size. This makes it hard to change the size of the simulation box in a RBFE calculation afais.

It would be best if Solventcomponent took a "buffer_size = 10*unit.Angstrom" parameter for building the box.

[IAlibay]

@steinbt2

Apologies, I'm not sure what happened with the showcase notebook, but that seems to be an error - at least ChemicalSystem cannot define the system properties.

There are two aspects to this currently.

1. Today, if you want to set the box vectors for "how the box will be solvated", you can do so via the SolvationSettings input to a Protocol: https://docs.openfree.energy/en/stable/reference/api/openmm_protocol_settings.html#openfe.protocols.openmm_utils.omm_settings.OpenMMSolvationSettings. Specifically you can set solvent_padding to do what I think you're looking to do.

2. In the near future, we are looking to move some of this to the Component system - at least we want for folks to be able to pass in pre-solvated systems (for membrane systems), which means that we will need to be able to deal with setting box dimensions.

[steinbt2]

Hi Irfan, thanks for the pointer, yes solvent_padding is what I was looking for. I am not sure if the box size should be more of a protocol setting or a component property, but requests for using preequilbrated systems, especially membrane ones, will certainly come. So I guess my request is to just correct the documentation. Kind Regards, Thomas

…

On Wed, Dec 4, 2024 at 2:38 PM Irfan Alibay ***@***.***> wrote: @steinbt2 <https://github.com/steinbt2> Apologies, I'm not sure what happened with the showcase notebook, but that seems to be an error - at least ChemicalSystem cannot define the system properties. There are two aspects to this currently. 1. Today, if you want to set the box vectors for "how the box will be solvated", you can do so via the SolvationSettings input to a Protocol: https://docs.openfree.energy/en/stable/reference/api/openmm_protocol_settings.html#openfe.protocols.openmm_utils.omm_settings.OpenMMSolvationSettings. Specifically you can set solvent_padding to do what I think you're looking to do. 2. In the near future, we are looking to move some of this to the Component system - at least we want for folks to be able to pass in pre-solvated systems (for membrane systems), which means that we will need to be able to deal with setting box dimensions. — Reply to this email directly, view it on GitHub <#1032 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A7WSJP6XJKSX2XATJRJGXVD2D4AXBAVCNFSM6AAAAABTABE3ECVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKMJXGQZDQNZSGM> . You are receiving this because you were mentioned.Message ID: ***@***.***>

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[IAlibay]

Thanks for the follow-up @steinbt2 - we just updated the notebook (removing that erroneous entry), and will follow-up with more details on how to set the solvation settings.

I'm going to close this issue as "completed" (or at least other issues have been opened elsewhere), but please do re-open it as necessary.