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Support 4-site water models in Amber export #783
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I'm trying to figure out how this is implemented in Amber files and I'm getting pretty confused pretty quickly.
I seem to be in good company with my confusion. Section 17.5 of the Amber22 manual begins
There's a lot of useful information in that chapter on how |
I'm still super perplexed at how the geometry of the virtual site is kept in place. There's a soft convention of adding a bond between the virtual site and its parent atom, which might constrain that particular distance, but what about the rest of the geometry? In other words, what's keeping the virtual site in 4-site water in the plane? |
I wonder if we can ask Jason Swails this? |
@swails could you suggest a starting point for us to understand how various engines within Amber expect to see virtual sites structured in files? I can't find a lot on the Amber website. I know |
Description
This should be simpler than implementing all virtual site types i.e. for ligands, I think.
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