1. Tracing the origin of the amide issue
...
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
...
v1.2.0 | fb-fit2 | fb-fit3 | fb-fit4 | full | |
|---|---|---|---|---|---|
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
...
(2) Test set 1
...
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 |
...
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.
...
4. Conclusions
Blah Blah
* Fitting torsion parameters to simpler torsion targets (with less strong electrostatic interaction) might be needed for the next round fitting.