1. Tracing the origin of the amide issue
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So one easy fix of the problem is using simple targets, whose torsion profiles have parabolic shape near the minimum (planar geometry at the minimum). + Expecting that this experiment to be one proof of the need for using simple-as-possible torsiondrive targets in general torsion parameter fitting.
2. Filtering non-planar structure at minimum geometry
(since the 2nd generation torsion training set is too small to filter, i pulled Roche torsion set (1st gen) and filtered with various scheme. )
scheme 2. check improper dihedral angles at the minimum energy point of the torsion profile, take targets whose C-center and N-center improper dihedral angles are both between -5.0, 5.0 degree;
scheme 3. check QM data to see if the profile has its local minima at 0 or 180;
scheme 4. targets passed either scheme 2 or scheme 3
maybe 2d image of molecules?
3. fb-fit2 vs. fb-fit4
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For the test set (amide-rotating Roche torsion targets which are not selected either from scheme 2 or from scheme 3), can’t see the effect of splitting endo-cyclic rotation and exo-cyclic rotation
Parameter sets fitted to scheme 2 and scheme 4 performs similarly, while the parameter set fitted to the scheme 4 slightly more prefer to form hump at the near-planar structure. (could be good or bad)
v1.2.0 | fb-fit2-2 | fb-fit3-2 | fb-fit4-2 | |
|---|---|---|---|---|
test cal. | 144.59 | 91.81 | now running | 88.84 |
final obj. fn. (fitting) | - | 1.31e+02 → 2.22e+01 | now running | 2.09e+02 → 3.01e+01 |
SMIRKS | initial guess | fb-fit2-2 | fb-fit4-2 | |
|---|---|---|---|---|
t69a | [*:1]-[#7X3:2]-[#6X3$(*=[#8,#16,#7]):3]~[*:4] | 2.5 (1+cos(2x-180)) | 1.679285484776e+00 (1+cos(2x-180)) | 1.778613695219e+00(1+cos(2x-180)) |
t70 | [#1:1]-[#7X3:2]-[#6X3:3]=[#8,#16,#7:4] | 3.459249459574e+00 (1+cos(2x-180)) + 1.356955617521e+00 (1+cosx) | 3.566161051804e-01 (1+cos(2x-180)) + 1.354248559088e+00 (1+cosx) | -1.357682774067e+00 (1+cos(2x-180)) + 1.266337423993e+00 (1+cosx) |
t70b | [*:1]-[#7X3:2]-!@[#6X3:3](=[#8,#16,#7:4])-[#6,#1] | 2.5 (1+cos(2x-180)) | 4.169159533591e+00 (1+cos(2x-180)) | 4.107144298045e+00(1+cos(2x-180)) |
t70c | [#1:1]-[#7X3:2]-!@[#6X3:3](=[#8,#16,#7:4])-[#6,#1] | 2.5 (1+cos(2x-180)) + 2.0 (1+cosx) | 1.240609067243e+00 (1+cos(2x-180)) + 9.065552775144e-01 (1+cosx) | 1.115929833406e+00(1+cos(2x-180)) + 7.646525300953e-01(1+cosx) |
t70d | [*:1]-[#7X3:2]-!@[#6X3:3](=[#8,#16,#7:4])-[#7X3] | 2.5 (1+cos(2x-180)) | 1.303139175986e+00 (1+cos(2x-180)) | 1.167960735598e+001+cos(2x-180)) |
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4. Conclusions and what-to-do-next
* Fitting torsion parameters to simpler torsion targets (with less strong electrostatic interaction) might be needed for the next round fitting.
* so irrelevent! (move to the new page with “the new priors selection”)
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