On Fri, Dec 13, 2024, VERONICA MARTIN HERNANDEZ via AMBER wrote:
>
>I'm performing TI calculations, and I've got more like a methodological
>question. I'm replacing a hydrogen to a fluorine, but both atoms have to
>share the same xyz coordinates? Because the distance carbon-hydrogen and
>carbon-fluorine aren't the same, so, to me, it's not logic that both atoms
>have the same coordinates, but I don't know
In the standard (non-softcore) approach, which should work fine for CH ->
CF, the distance between the two atoms changes as you go from lambda=0 to
lambda=1. So the end points have the proper bond distances. At
intermediate lambda values, the system is in a "mixed" state, which is not
required to be physical.
...hope this helps....dac
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Received on Sat Dec 14 2024 - 08:00:03 PST
