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Add a ring opening/closing test case #42

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jchodera opened this issue Nov 16, 2015 · 5 comments
Closed

Add a ring opening/closing test case #42

jchodera opened this issue Nov 16, 2015 · 5 comments
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@jchodera
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The null transformation of naphthalene to naphthalene (where a ring is destroyed at one end and created at the other end) would be a great test case since we know the free energy difference should be zero. (Jed Pitera had a paper on this test case with Wilfred van Gunsteren.). We can do this in vacuum, implicit solvent, and explicit solvent.

This would be a very powerful test because of the novelty of our ability to handle ring opening and closing.

@jchodera
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Jed's naphthalene paper is here: http://dx.doi.org/10.1080/08927020211973

@jchodera
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I've already implemented this test case.

@jchodera
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jchodera commented Sep 20, 2016

Whoops, my mistake: I only implemented benzene <-> napthalene, not the naphthalene null transformation (which would require specifying the atom mappings to use).

@pgrinaway
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Yeah, I almost made the same mistake and closed the issue, but you're right.

@pgrinaway
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These are in the repo.

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