Page Comparison

Note: This post will be moved to Force Field / FF releases / Parsley minor release(s) once it is ready to be shared.

Fitting Data and Results

• Fitting targets: 2nd generation training sets (link for the details of the training set generation scheme: http://doi.org/10.5281/zenodo.3777278)

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• Three angle terms with noticeably different k values between RC1 and RC2:

  • a6([#1:1]-[*;r3:2]~;!@[*:3], k value in SMIRNOFF99Frosst: 100 kcal/mol/radian²)

  • a3([*;r3:1]1~;@[*;r3:2]~;@[*;r3:3]1, k value in SMIRNOFF99Frosst: 200 kcal/mol/radian²)

  • a15([#8X1:1]~[#6X3:2]~[#8:3], k value in SMIRNOFF99Frosst: 126 kcal/mol/radian²)

: Based solely on intuition, RC2 angle k values for the angle terms(doesn’t change much from the k value in 1.1.0 throughout the optimization) seem physical; 400kcal/mol/radian² (final k value in RC1) for angle seems too large compare to other angle k values. Final gradients for the angle k values are also higher in RC1 (a6: 5.580e+00 , a15 : 4.750e+00) compared to the gradients in RC2 (a6: 1.599e+00 , a15 : 1.391e+00)

: Scatter plots seem slightly better in RC1. Also one thing I noticed is that large initial guess of a15 equilibrium angle has been used in RC2 fitting, which led to larger final equilibrium angle(~135 degree) compared to the final equilibrium angle in RC1(~ 129 degree). (a15 equilibrium angle in v1.1.0 is around 137 degree, which is larger than angles observed in QM optimized geometries.)

( The issue with converging to a final equilibrium value substantially off from values in QM optimized geometries is one of the known issues that we are currently working on. )

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Cf. But it seems like having final equilibrium angle different with QM values is not always the case we want to avoid. Here’s one example. As you can see in the scatter plot below, the fitting converged to a larger a38 equilibrium angle (~ 147 degree) which is larger than QM values(~ 110 degree). And the large equilibrium angle has been found to be beneficial in locating hydroxyl hydrogen in phosphono group far away enough from its neighboring oxygens, preventing unphysical intermolecular H-bonding between the hydrogen and the neighbor oxygens.

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• Three torsion terms with significantly different final k values between RC1 and RC2:

  • t146, t147: having 6 cosine functions

  • t15 ([*:1]-[#6X4;r3:2]-@[#6X4;r3:3]-[*:4]), t16 ([#6X4;r3:1]-[#6X4;r3:2]-[#6X4;r3:3]-[*:4]): in-ring rotations

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(2) v1.2.0-RC1 vs. v1.2.0-RC2: Comparison of RMSD for each parameter

RC2 decrease RMSD of internal coordinates assigned to t135, t146, t34 and t97 while increasing RMSDs for t54 and t55.

(3) v1.2.0-RC1 vs. v1.2.0-RC2: Optimized geometries

Specific improvement in optimized geometries with certain functional groups(phosphono group, sulfamate acetate) found in RC1 is also shown in RC2.

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QM optimized geometry of CC(O)([P@@](=O)(O)[O-])[P@](=O)(O)[O-]. ( orange: MM optimized geometry with v1.1.0 force field, green: v1.2.0-RC1 force field, magenta: v1.2.0-RC2 force field)

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4) v1.2.0-RC1 vs. v1.2.0-RC2: Relative energies between conformers at “QM optimized geometries”

Performance comparison of RC1 and RC2 in reproducing QM relative energies between conformers was carried out. Two different ways to calculate MM relative energies were used. In the first approach, MM relative energies were calculated by subtracting MM energy at the QM minimum from MM energy at each point (distribution figure on the left). Second approaches calculated MM relative energies by subtracting MM energy at QM minimum from MM energy at each point(distribution figure on the right). Both candidates have smaller MAD and shorter tails than v1.1.0, indicating slight better performances over v1.1.0, while RC2 shows a slightly better performance over RC1.

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+ v1.2.0-RC1 vs. v1.2.0-RC2:

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Molecules having [#7X2]-!@[#7X3]

RC2 is slightly worse than RC1 in reproducing QM optimized geometries (RMSD and TFD) while showing slightly better performance in reproducing QM energetics (ddE)

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*Figures will be trimmed soon!