(1) 2020-08-27 valence parameter test re-fitting for fixing amide issue

1. new t70 child parameter candidate

t68(pre-existing)

[*:1]~[#7X3,#7X2-1:2]-[#6X3:3]~[*:4]

t69(pre-existing)

[*:1]~[#7X3,#7X2-1:2]-!@[#6X3:3]~[*:4]

t70at69a

[*:1]-[#7X3:2]-!@[#6X3$(*=[#8,#16,#7]):3]~[*:4] ( - or -!@?)

t70(pre-existing)

[#1:1]-[#7X3:2]-[#6X3:3]=[#8,#16,#7:4] ( - or -!@?)

t70a

[*:1]-[#7X3:2]-!@[#6X3:3](=[#8,#16,#7:4])-[#6,#1]

t70b

[#1:1]-[#7X3:2]-!@[#6X3:3](=[#8,#16,#7:4])-[#6,#1]

t70c

[*:1]-[#7X3:2]-!@[#6X3:3](=[#8,#16,#7:4])-[#7X3]

cf. Barrier height study (mainly for my own understanding) to understand (1) why we need child terms t70a and t70b .

- Conclusion: Based on the following plots, it seems reasonable to have separate child term [*:1]-[#7X3:2]-!@[#6X3:3](=[#8,#16,#7:4])-[#1] (higher energy barrier) and [*:1]-[#7X3:2]-!@[#6X3:3](=[#8,#16,#7:4])-[#7X3] ( lower energy barrier).

- No clear evidence for the necessity to combine a pattern with carbon attached to the carbonyl carbon ([*:1]-[#7X3:2]-!@[#6X3:3](=[#8,#16,#7:4])-[#6]) and one with hydrogen attached to the carbonyl carbon([*:1]-[#7X3:2]-!@[#6X3:3](=[#8,#16,#7:4])-[#1])

2. Test fitting

(1) re-fitting #1.1

  • Separated endo-cyclic and exo-cyclic rotations( t69a and t69b, t70 and t70a): will determine whether to separate or not after comparing the final k values.

  • w/ only selected td targets

  • w/ old conda env.(openforcefield==0.6.0, forcebalance=1.7.1)

  • optimized in 6 steps (3.21033e+01 → 7.97182e+00)

 

SMIRKS
 

 initial guess

fit #1.1

 

SMIRKS
 

 initial guess

fit #1.1

t69a 

[*:1]-[#7X3:2]-[#6X3$(*=[#8,#16,#7]):3]~[*:4]

2.5 (1+cos(2x-180))  + 0.0 (1+cosx)

2.130536422094e+00 (1+cos(2x-180))  + 9.910621243621e-02 (1+cosx)

t69b

[*:1]-[#7X3:2]-!@[#6X3$(*=[#8,#16,#7]):3]~[*:4]

2.5 (1+cos(2x-180)) + 0.0 (1+cosx)

2.270075197860e+00 (1+cos(2x-180))  + 3.898905433309e-01 (1+cosx)

t70

[#1:1]-[#7X3:2]-[#6X3:3]=[#8,#16,#7:4]

3.459249459574e+00 (1+cos(2x-180))  + 1.356955617521e+00 (1+cosx)

3.471614493904e+00 (1+cos(2x-180))  + 1.353665035664e+00 (1+cosx)

t70a

[#1:1]-[#7X3:2]-!@[#6X3:3]=[#8,#16,#7:4]

2.5 (1+cos(2x-180))  + 2.0 (1+cosx)

2.5 (1+cos(2x-180))  + 2.0 (1+cosx)

t70b

[*:1]-[#7X3:2]-!@[#6X3:3](=[#8,#16,#7:4])-[#6,#1]

2.5 (1+cos(2x-180))  + 0.0 (1+cosx)

2.779138641990e+00 (1+cos(2x-180))  + 3.381053683048e-02 (1+cosx)

t70c

[#1:1]-[#7X3:2]-!@[#6X3:3](=[#8,#16,#7:4])-[#6,#1]

2.5 (1+cos(2x-180))  + 2.0 (1+cosx)

2.590468938026e+00 (1+cos(2x-180))  + 1.820091344671e+00 (1+cosx)

t70d

[*:1]-[#7X3:2]-!@[#6X3:3](=[#8,#16,#7:4])-[#7X3]

2.5 (1+cos(2x-180))  + 0.0 (1+cosx)

1.888086753838e+0 (1+cos(2x-180)) - 2.028808021603e-01 (1+cosx)

  • QM vs MM torsion profiles