1. Tracing the origin of the amide issue
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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 out non-planar
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structures at the minimum geometry
Several schemes to filter non-planar molecules:
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(Since the 2nd generation torsion training set is too small to filter, i pulled Roche torsion set (1st generation) and filtered with various scheme. )
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Test set 1: (1) the simplest molecule, N-methyacetamide, (2) non-planar molecules filtered out in both scheme 2 and scheme 3;
Test set 2: all amide torsions in the 2nd generation training dataset;
Overall quality of fitting and test calculation:
v1.2.0 | fb-fit2 (scheme 2) | fb-fit3 (scheme3) | fb-fit4 (scheme 4) | full Unfiltered | |
|---|---|---|---|---|---|
test cal 1 | 144.59 | 91.81 | 82.39 | 88.84 | - |
test cal 2 | 25.37 | 15.62 | 14.75 | 14.15 | 23.21 |
test cal 2-1 simple | 7.10 | 6.21 | 7.49 | 8.29 | 11.04 |
test cal 2-2 complex | 18.26 | 9.40 | 7.26 | 6.87 | 12.17 |
final X2 (fitting) | - | 1.31e+02 → 2.22e+01 | 1.30e+02 → 1.73e+01 | 2.09e+02 → 3.01e+01 | 5.28e+02 → 6.90e+01 |
(1) N-methylacetamide
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(2) Test set 1 (N-methyacetamide, non-planar molecules in the 1st gen. Roche torsion set)
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(3) Test set 2
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(All amide torsions in the 2nd gen. training set)
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(4) Check performance on non-planar molecules
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(5) Direct comparison of final parameters
F(θ) = k1*(1+cos(2θ-180)) + k2*(1+cosθ)
ID, SMIRKS | Initial guess | fb-fit2 | fb-fit3 | fb-fit4 |
|---|---|---|---|---|
| k1 = 2.5 | k1= 1.6793e+0 | k1 = 1.3647e+0 | k1 = 1.7786e+0 |
| k1 = 3.4592e+0 k2 = 1.3570e+0 (from 1.2.0) | k1 = 3.5662e-1 k2 =1.3542e+0 | k1 = 2.4868e-1 K2 = 9.4280e-1 | k1 = -1.3577e+0 k2 = 1.2663e+0 |
| k1 = 2.5 | k1 = 4.1692e+0 | k1 = 4.4151e+0 | k1 = 4.1071e+0 |
| k1 = 2.5 k2 = 2.0 | k1 = 1.2406e+0 k2 = 9.0656e-1 | k1 = 1.5283e+0 k2 = 7.3406e-1 | k1 = 1.1159e+0 k2 = 7.6465e-1 |
| k1 = 2.5 | k1= 1.3031e+0 | k1 = 1.6149e+0 | k1 = 1.1680e+0 |
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* About the counter-intuitive negative k1 value of t70, [#1:1]-[#7X3:2]-[#6X3:3]=[#8,#16,#7:4]
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Although the k1 value for t70a seems unphysical, the result below shows the plots got improved after the optimization. checked improvement for all of the four fitting targets.
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4. Conclusions
Blah Blah
* Fitting torsion parameters to simpler torsion targets (with less + Selecting simple geometries (no strong electrostatic interaction) might be needed for the next round fittingmay need to be considered in the next torsion training dataset selection procedure.