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 non-planar structure at minimum geometry
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3. Comparison of different filtering schemes
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Parameter sets fitted to Test set 1: (1) the simplest molecule, N-methyacetamide, (2) non-planar molecules filtered out in both 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)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 | fb-fit3 | fb-fit4 | ||
|---|---|---|---|---|---|
test cal 1 | 144.59 | 91.81 | 82.39 | 88.84 | |
test cal 2 | 25.37 | 15.62 | 14.75 | 14.15 | |
test cal 2-1 simple | 7.10 | 6.21 | 7.49 | 8.29 | |
test cal 2-2 complex | 18.26 | 9.40 | 7.26 | 6.87 | |
final X2 (fitting) | -1.31e+02 → 2.22e+01 | 1.30e+02 → 1.73e+01 | 2.09e+02 → 3.01e+01 |
(1) N-methylacetamide
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(2) Test set 1
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(3) Test set 2
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(4) Check performance on non-planar molecules
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(5) Direct comparison of final parameters
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 |
f(x) = k1*(1+cos(2θ-180)) + k2*(1+cosθ)
* 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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* after fitting to planar molecules , does the force field force the non-planar molecules planar??
td_OpenFF_Group1_Torsions_071_C14H13NO- one example of molecules, which is non-planar at the minimum
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4. Conclusions
Blah Blah
* Fitting torsion parameters to simpler torsion targets (with less strong electrostatic interaction) might be needed for the next round fitting.