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Version 1.1.0 "Parsley" Update (March 03, 2020)

Posted on 3 Mar 2020 by Hyesu Jang

Description

We are pleased to announce the release of our first “Parsley” update. Version 1.1.0 “Parsley” is a minor release that includes some adjustments in force field: (1) Addition of three new bond and angle terms, a22a, b14a and b36a; (2) Modification of periodicity for N-N rotations; (3) Addition of missing improper torsions (i2a, i3a, i3b, i5a) with the associated torsions (t51a,t51b, t51c); and (4) Removal of redundant periodicity in t19.

Datasets for parameterization

  • Roche set:: 686 1-D torsion profiles; 936 optimized geometries; 669 vibrational frequencies
  • Coverage set:: 412 1-D torsion profiles; 842 optimized geometries; 265 vibrational frequencies
  • Additional 19 1-D torsion profiles

Re-fitting Result

Details of the re-fitting result can be found in v1.1.0 release note.

  • Modification of periodicity for N-N rotation introduces significant improvement in reproducing QM optimized geoemetries of molecules having conjugated N-N bonds.

N-N-torsions

  • Addition of missing improper torsions and their associated torsions fixes the problem with reproducing QM optimized geometry of tetrazole.

NEt-tetrazole

Benchmark Results

Benchmark results show that there is a slight improvement on reproducing QM optimized geometries and reproducing relative energies between conformers. Details of the benchmark results can be found in v1.1.0 release note.

The weighted root-mean-square error (WRMSE) of each molecule, which is weighted root-mean-square deviation between internal coordinates of MM optimized geometry and QM optimized geometry was calculated for each parameter set then comparison of the WRMSE values was carried out.

wrmse-v1.1.0

Figure 1. Weighted root-mean-square deviation (WRMSE) between internal coordinates of MM optimized geometry and QM optimized geometry. The values on y-axis in the left plots (Δ WRMSE) are the changes in the WRMSE from initial force field to optimized force field – negative y values indicate better reproduction in the optimized force field compared to initial force field.

avgErr-v.1.1.0

Figure 2. Absolute QM vs MM relative energy differences averaged over conformers were calculated for each parameter set. The values on y-axis in the left plots (Δ Averaged Error) are the changes in averaged error of from initial force field to optimized force field – negative y values indicate better reproduction in the optimized force field compared to initial force field.