Sage 2.1

Owned by Lily Wang
Last updated: Jun 29, 2023
2 min read

Experiment Category

Step

Each step requires the previous step's FF.offxml as a reference

Decision

  • INCLUDE: The point release includes this step

  • SKIP: This step will be ignored or tried again later

Status

  • OPEN: Not started

  • IP: In progress

  • DONE: Conclusion reached

Optionally tag people if status is in progress or done

FF.offxml

Place the offxml file of the result here

Only put the offxml file of the “official” fit, not the independent/exploratory test; place those in the notes

Notes/Links to background

Motivation, reports, and information regarding why the step is needed

Passing Criteria

Tests available to determine if step was successful

RMSD
TFD
DDE

Experiment Category

Step

Each step requires the previous step's FF.offxml as a reference

Decision

  • INCLUDE: The point release includes this step

  • SKIP: This step will be ignored or tried again later

Status

  • OPEN: Not started

  • IP: In progress

  • DONE: Conclusion reached

Optionally tag people if status is in progress or done

FF.offxml

Place the offxml file of the result here

Only put the offxml file of the “official” fit, not the independent/exploratory test; place those in the notes

Notes/Links to background

Motivation, reports, and information regarding why the step is needed

Passing Criteria

Tests available to determine if step was successful

RMSD
TFD
DDE

1 Chemistry specific (from reported discrepancies)

A. Chloro compounds

OPEN @Pavan Behara

 

 

RMSD
TFD
DDE

B. Vehicle set bridgehead nitrogens

IP @Pavan Behara

 

 

RMSD
TFD
DDE

C. Nitrogen-oxygen bonds in constrained systems (ring-like) - fails in MM

IP @Pavan Behara

 

 

RMSD
TFD
DDE

D. Bicyclo pentane moieties - fails in MM

open @Pavan Behara

 

 

RMSD
TFD
DDE

 

E. Disagreement in torsion profiles

 

 

 

https://docs.google.com/presentation/d/1p17ZvmOxXY8fXggCN9ygplS85fQBE2dAEv8tDTUIS94/edit?usp=sharing

 

 

F. Missing parameters

 

Missing parameters in current force field

 

 

 

2 Changing fitting protocol

A Modifying torsion parameters to fit optimized geometries

IP @Pavan Behara

 

/dfs6/pub/pbehara/fitting-exp-dfs6/iter0/dih_denom_included/result/optimize

B. Starting from a different reference: QM estimated values

OPEN @Pavan Behara

 

/dfs6/pub/pbehara/fitting-exp-dfs6/iter2/result/optimize

priors are different here, may need a rerun

A + B

 

 

 

 

 

C. Penalize all torsion k’s to zero

OPEN

 

 

D. Reintroduce hessian info via ICH target

OPEN @Pavan Behara

 

 

 

E. Reduced set of optimization targets

 

@Pavan Behara

 

/dfs6/pub/pbehara/fitting-exp-dfs6/iter18

 

3 Torsions

A.

  • Reassess all periodicities: full reset

  • Reassess all periodicities: add missing

OPEN

 

https://docs.google.com/presentation/d/1p17ZvmOxXY8fXggCN9ygplS85fQBE2dAEv8tDTUIS94/edit?usp=sharing

OPEN

 

 

B. torsion multiplicity: explicit valence torsions set

IP @Jessica Maat (Deactivated)

 

 

 

C. Remove phase angles 90/270 from current FF

 

 

 

 

 

4 Impropers

A. fitting current impropers

OPEN @Pavan Behara

 

 

B. finding new impropers for i4

OPEN

 

 

C. double-well functional form

IP @Pavan Behara

 

 

5 WBO interpolated parameters

A. Torsion for biphenyl-ortho-unsubstituted

OPEN @Pavan Behara

 

 

 

B. Trivalent Nitrogen improper

TODO

 

 

6 Angles/Bonds

A. Improved general parameters from automated-chemical-perception

IP @Trevor Gokey

 

 

Benchmarks/Tests