Linear vs. cyclic alkanes with a simple FF
A simple force field for alkanes with bond and angle parameters being:
b1: [#6X4:1]-[#6X4:2]
b83: [#6X4:1]-[#1:2]
a1: [*:1]~[#6X4:2]-[*:3] matches CCC, CCH
a2: [#1:1]-[#6X4:2]-[#1:3] matches HCH
For the angle parameters the mean, max and min for different sets of alkanes from the QM data:
acyclic | Mean | Max | Min |
a1 | 110.47 | 114.53 | 108.69 |
a2 | 107.42 | 109.48 | 105.99 |
cyclic | Mean | Max | Min |
a1 | 109.77 | 118.01 | 59.99 |
a2 | 106.79 | 114.38 | 105.00 |
both | Mean | Max | Min |
a1 | 110.02 | 118.01 | 59.99 |
a2 | 107.15 | 114.38 | 105.00 |
Different fits:
1. With priors (same as 1.2, penalty_additive 1.0)
With priors (same as 1.2, penalty_additive 1.0) | Initial values | both | cyclic | acyclic | Std. Dev | Openff_1.3.0 |
b1, length, [#6X4:1]-[#6X4:2] | 1.0 | 1.5 | 1.5 | 1.5 | 0.02 | 1.5 |
b1, k, [#6X4:1]-[#6X4:2] | 500.0 | 488.8 | 487.6 | 487.7 | 0.53 | 517.2 |
b83, length, [#6X4:1]-[#1:2] | 1.0 | 1.1 | 1.1 | 1.1 | 0.00 | 1.1 |
b83, k, [#6X4:1]-[#1:2] | 700.0 | 699.9 | 699.9 | 699.9 | 0.01 | 754.1 |
a1, angle, [*:1]-[#6X4:2]-[*:3] | 113.7 | 108.9 | 109.2 | 104.9 | 1.93 | 113.7 |
a1, k, [*:1]-[#6X4:2]-[*:3] | 99.2 | 83.1 | 88.5 | 112.9 | 12.97 | 99.2 |
a2, angle, [#1:1]-[#6X4:2]-[#1:3] | 90.0 | 105.5 | 105.4 | 94.1 | 5.35 | 114.3 |
a2, k, [#1:1]-[#6X4:2]-[#1:3] | 60.0 | 93.4 | 96.2 | 42.2 | 24.78 | 66.6 |
X2 value |
| 2.948394e+01 | 2.891730e+01 | 2.550521e+01 |
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2. w/o priors (penalty_additive 0.0;penalty_multiplicative -1.0)
w/o priors (penalty_additive 0.0;penalty_multiplicative -1.0) | Initial values | both | cyclic | acyclic | Std. Dev | Openff_1.3.0 |
b1, length, [#6X4:1]-[#6X4:2] | 1.0 | 1.5 | 1.5 | 1.5 | 0.00 | 1.5 |
b1, k, [#6X4:1]-[#6X4:2] | 500.0 | 521.1 | 1279.4 | 1106.4 | 324.47 | 517.2 |
b83, length, [#6X4:1]-[#1:2] | 1.0 | 1.1 | 1.1 | 1.1 | 0.00 | 1.1 |
b83, k, [#6X4:1]-[#1:2] | 700.0 | 699.2 | 590.9 | 153.2 | 236.03 | 754.1 |
a1, angle, [*:1]-[#6X4:2]-[*:3] | 113.7 | 120.4 | 123.4 | 88.7 | 15.70 | 113.7 |
a1, k, [*:1]-[#6X4:2]-[*:3] | 99.2 | 72.9 | 62.7 | 59.4 | 5.75 | 99.2 |
a2, angle, [#1:1]-[#6X4:2]-[#1:3] | 90.0 | 117.0 | 119.3 | 88.1 | 14.20 | 114.3 |
a2, k, [#1:1]-[#6X4:2]-[#1:3] | 60.0 | 71.8 | 66.4 | 63.4 | 3.46 | 66.6 |
X2 value |
| 6.137531e-01 | 1.258127e+00 | 6.963839e-02 |
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3. With priors (same as 1.2, penalty_additive 1.0), initial values same as 1.3.0
With priors (same as 1.2, penalty_additive 1.0), initial values same as 1.3.0 | Initial values | both | cyclic | acyclic | Std. Dev | Openff_1.3.0 |
b1, length, [#6X4:1]-[#6X4:2] | 1.5 | 1.5 | 1.5 | 1.5 | 0.0 | 1.5 |
b1, k, [#6X4:1]-[#6X4:2] | 517.2 | 517.6 | 517.6 | 517.3 | 0.2 | 517.2 |
b83, length, [#6X4:1]-[#1:2] | 1.1 | 1.1 | 1.1 | 1.1 | 0.0 | 1.1 |
b83, k, [#6X4:1]-[#1:2] | 754.1 | 754.1 | 754.1 | 754.1 | 0.0 | 754.1 |
a1, angle, [*:1]-[#6X4:2]-[*:3] | 113.7 | 117.1 | 117.4 | 114.6 | 1.2 | 113.7 |
a1, k, [*:1]-[#6X4:2]-[*:3] | 99.2 | 74.4 | 78.0 | 94.8 | 8.9 | 99.2 |
a2, angle, [#1:1]-[#6X4:2]-[#1:3] | 114.3 | 113.3 | 113.8 | 113.1 | 0.3 | 114.3 |
a2, k, [#1:1]-[#6X4:2]-[#1:3] | 66.6 | 78.8 | 80.1 | 64.5 | 7.1 | 66.6 |
X2 value |
| 9.589902e-01 | 8.044047e-01 | 1.657006e-01 |
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4. w/o priors (penalty_additive 0.0;penalty_multiplicative -1.0), initial values same as 1.3.0
w/o priors (penalty_additive 0.0;penalty_multiplicative -1.0), initial values same as 1.3.0 | Initial values | both | cyclic | acyclic | Std. Dev | Openff_1.3.0 |
b1, length, [#6X4:1]-[#6X4:2] | 1.5 | 1.5 | 1.5 | 1.5 | 0.0 | 1.5 |
b1, k, [#6X4:1]-[#6X4:2] | 517.2 | 972.8 | 1353.2 | 1148.0 | 155.5 | 517.2 |
b83, length, [#6X4:1]-[#1:2] | 1.1 | 1.1 | 1.1 | 1.1 | 0.0 | 1.1 |
b83, k, [#6X4:1]-[#1:2] | 754.1 | 304.4 | 579.8 | 153.3 | 176.6 | 754.1 |
a1, angle, [*:1]-[#6X4:2]-[*:3] | 113.7 | 120.8 | 123.4 | 88.6 | 15.8 | 113.7 |
a1, k, [*:1]-[#6X4:2]-[*:3] | 99.2 | 59.2 | 62.8 | 59.6 | 1.6 | 99.2 |
a2, angle, [#1:1]-[#6X4:2]-[#1:3] | 114.3 | 115.1 | 119.3 | 88.0 | 13.8 | 114.3 |
a2, k, [#1:1]-[#6X4:2]-[#1:3] | 66.6 | 75.4 | 66.6 | 63.7 | 5.0 | 66.6 |
X2 values |
| 7.679078e-01 | 6.136701e-01 | 6.960467e-02 |
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5. With priors (same as 1.2, penalty_additive 1.0), repeating iteration 1 optimizing only angles
Initial values | both | cyclic | acyclic | Std. Dev | Openff_1.3.0 | |
a1, angle, [*:1]-[#6X4:2]-[*:3] | 113.7 | 108.5 | 108.5 | 105.0 | 1.7 | 113.7 |
a1, k, [*:1]-[#6X4:2]-[*:3] | 99.2 | 75.3 | 76.9 | 104.7 | 13.5 | 99.2 |
a2, angle, [#1:1]-[#6X4:2]-[#1:3] | 114.3 | 105.2 | 104.7 | 93.4 | 5.4 | 114.3 |
a2, k, [#1:1]-[#6X4:2]-[#1:3] | 66.6 | 90.1 | 91.6 | 39.8 | 24.1 | 66.6 |
X2 values |
| 1.978416e+00 | 1.802865e+00 | 4.377341e-01 |
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6. With initial values close to 1.3.0,
since above iterations seem to optimize to a local minima (thanks to Trevor for pointing that out in our discussion)
From both the fits below it seems only equilibrium force constant is going higher and changes in equilibrium angles are low when cyclic and acyclic optgeo targets are considered during optimization.
6a.) Optimizing both bonds and angles
With priors (same as 1.2, penalty_additive 1.0) | Initial values | both | cyclic | acyclic | Std. Dev | Openff_1.3.0 |
b1, length, [#6X4:1]-[#6X4:2] | 1.4 | 1.5 | 1.5 | 1.5 | 0.01 | 1.5 |
b1, k, [#6X4:1]-[#6X4:2] | 500.0 | 498.2 | 498.0 | 498.1 | 0.06 | 517.2 |
b83, length, [#6X4:1]-[#1:2] | 1.0 | 1.1 | 1.1 | 1.1 | 0.00 | 1.1 |
b83, k, [#6X4:1]-[#1:2] | 740.0 | 739.9 | 739.9 | 739.9 | 0.00 | 754.1 |
a1, angle, [*:1]-[#6X4:2]-[*:3] | 110.0 | 114.0 | 114.2 | 111.3 | 1.32 | 113.7 |
a1, k, [*:1]-[#6X4:2]-[*:3] | 98.0 | 74.1 | 77.4 | 94.1 | 8.72 | 99.2 |
a2, angle, [#1:1]-[#6X4:2]-[#1:3] | 110.0 | 110.2 | 110.4 | 108.7 | 0.78 | 114.3 |
a2, k, [#1:1]-[#6X4:2]-[#1:3] | 65.0 | 84.6 | 85.8 | 64.9 | 9.61 | 66.6 |
X2 values |
| 3.497131e+00 | 3.342547e+00 | 2.413090e+00 |
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6b.) Optimizing only angles
With priors (same as 1.2, penalty_additive 1.0) | Initial values | both | cyclic | acyclic | Std. Dev | Openff_1.3.0 |
a1, angle, [*:1]-[#6X4:2]-[*:3] | 110.0 | 114.1 | 114.3 | 111.3 | 1.3 | 113.7 |
a1, k, [*:1]-[#6X4:2]-[*:3] | 98.0 | 75.8 | 78.5 | 93.1 | 7.6 | 99.2 |
a2, angle, [#1:1]-[#6X4:2]-[#1:3] | 110.0 | 110.3 | 110.5 | 108.6 | 0.9 | 114.3 |
a2, k, [#1:1]-[#6X4:2]-[#1:3] | 65.0 | 85.2 | 86.0 | 64.7 | 9.9 | 66.6 |
X2 values |
| 1.174437e+00 | 1.016303e+00 | 1.800063e-01 |
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