how use it to calculate osmotic permeability

giorginolab / vmd_diffusion_coefficient

Computing Diffusion Coefficients in Macromolecular Simulations: The Diffusion Coefficient Tool for VMD

https://doi.org/10.21105/joss.01698

BSD 3-Clause "New" or "Revised" License

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how use it to calculate osmotic permeability #15

Closed groponp closed 1 year ago

groponp commented 1 year ago

Dear I'm intereset into know if it algorithm enable calculate pf (osmotic permeability) to measure water transport into aquaporins

tonigi commented 1 year ago

I doubt it is possible without adaptations.

groponp commented 1 year ago

Dear, Sorry that the question is basic, but how can I select the water molecules that are inside a monomer of my aquaporin, since when I make a selection using for example "waters and z >=-9 and z < 9" if I do not apply an update of the selection, everything looks scattered and I don't really see the molecules in the channels, like I see them if I just do "waters".

I would appreciate any suggestions.

tonigi commented 1 year ago

No, currently updating the selection at every frame is not supported (because the number of atoms would change).