JW: What range is H stretching? (re frequency data)
TG: around 3000-3500 cm-1
JW: Most people use constrained FF, so H stretch isn’t too important. Issue is with lower frequencies
TG: Bonds in 3000 range aren’t only C-H bonds, it’s all bonds. Those errors aren’t unimportant
CB: Resonance frequency issue with C#C-CH3 triple bond that caused explosions. Other triple bonds are C#N, maybe one other….should be around 2500. Generally worried about resonance frequencies, plotting like this would help identify
TG: What do you mean by resonance
CB: Reason that H bond are constrained is because MD timestep is close to frequency of CH bond, leads to explosion in energies during MD. Depending on timestep, could happen with other bonds
JW: Wouldn’t see same issue with triple bond, because in those simulations we used HMR which lowers mass of C. So wouldn’t show up here, with genuine masses.
CB Could recalculate these frequencies using scaled down HMR mass
JW--could be good topic for FF release meeting, could be an addition into release process
CB what other bonds besides H have frequency over 3000?
TG rings with two N’s triple bonded or other N#N, force constant 3300.
CB also cyclopropyls, still looking into the cyclopropyl resonance
TG good point that this could be useful for identifying resonance frequencies
PB--Last time you also showed difference from MSM, did you check that?
TG--no, too many molecules, didn’t check. But Sage is very close to MSM. Sage underestimates bonds but does angles well.
TG--using vibrational modes of QM, not minimizing MM structure beforehand. There is a white blank space line in frequency plots, anything closer to y axis is a negative frequency (MM isn’t at minimum)
CB--is that a meaningful thing to calculate? Second derivative wouldn’t necessarily be comparable at minimum vs not minimum?
TG--If you minimized, just because you got same FC wouldn’t mean same vibrational mode, could be same eigenvalue but not same eigenvector
CB--but now you have same eigenvector but not necessarily meaningful eigenvalue
TG--have to make tradeoffs and decide what is better
LM--you suggested incorporating this into fitting pipeline, what aspect would you incorporate?
TG--idea would be to replace MSM with something like this
CB--Hessians come from QM min, right?
TG--yes
CB-- That would inform the fit, especially the torsions. Would inform FC of bonds and angles (single minimum per conformer). However, for torsions, a much better description of minimum would change description of barrier in addition to FC. Would it make it better or worse?
TG--good point, I was first looking at description of minimum, before looking at other points on PES like barrier.
CB--Fitting the Hessian at any point would also affect all targets
CB--are you using torsion drives?
TG--no, want to see how well we can do looking only at minima before using exotic properties/conformers
TG--Chris, what’s your opinion on Sage frequencies being overestimated for torsions? Got same result for Frosst
CB--Definitely not a planned feature. I didn’t know it, but not necessarily surprised
CB--Just speculating here. All our FFs do torsion parameterization as though torsions are independent, but know that there is a strong correlation between adjacent torsions. Could be outcome of not considering correlation/dependence between terms (“diagonal” FF). This is where that would show up
CB--Makes me nervous that you aren’t using MM minimum for frequencies, QM hessian includes anharmonic features which we can’t capture with a “diagonal” FF
TG--In general, there are a few negative frequencies, usually except for pathological cases they are low eg -100/-200 cm-1
CB--Could be good to check using MM minimum for small subset of dataset
TG--problem would be matching the vibrational mode for comparison
LW--Diagonal lines for bonds, looks like Sage is predicting two averaged values so half are below and half are above. Wonder what the reason is.
JW--is your FF coming up with a bunch of H bond parameters? Or just 3?
TG--Using Sage SMARTS, not changing the patterns
CB--See recording around 47 min, shares some details about which bonds are in which frequency ranges
CB--not seeing alkane CH on this plot, but might be constrained
TG--can pass on re-set Sage parameters for fitting team to re-fit, and am also trying to re-fit myself
CB--is MSM using hessian to get FC?
TG--Yes
CB--So, a similar method. Do you think including this info would make result closer to MSM?
TG--No, they land in different local minima. MSM is very local, e.g. for a bond it only sees the two atoms that are bonded. This uses pseudo-inverse of B, which means it’s aware of all the internal coordinates