| TG | JR: BS and I had to symmetrize some molecules by hand in a previous project DM: GAFF does this on purpose because otherwise the bridgehead carbons get different parameters TG: just to clarify, did you symmetrize the SMARTS? JR: we went in by hand and ensured h1 got the same parameter as h2 (on “SMARTS mimics GAFF for nearly all types”)
(“Results fixed outliers and overall frequencies”) LW: which molecules is mol36? JR: how large are the frequencies producing these MAEs? JR: you’re just fitting to a Hessian, not the next level up in the Taylor series, right? TG: I’m using a simple class I FF here, we could likely improve results if we extended it BS: the NEB has a stiffness parameter. If that’s looser, would the NEB pathway look more like the others? TG: I don’t think so. The nudged part of NEB is that it projects out the parallel component of the force, so that the force between two images is the spring. The choice of the spring constant shouldn’t matter, as the molecular component is always projected out. BS: So the NEB pathway is meant to be a minimum energy pathway of sorts?
JR: … TG: the metadynamics calls it free energy but it’s still gas phase sampling through space, not a gibbs free energy JR: would recommend using a dispersion-modified functional, like B3LYP-D3*.
LW: how well do you think NEB would generalize well over a larger dataset? BS: how do you find the minima to interpolate?
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