Structural benchmark to validate new dihedrals equation

[martimunicoy]

Description

The purpose of this benchmark is to fully validate the implementation of the new dihedrals equation to make PELE compatible with openFF (issue with more details).

Workflow

• Take several structures from QCPortal that have been optimized with QM.
• Filter structures to keep only those that employ one of the OpenFF dihedrals with a non null phase constant.
• Save optimized structures to PDB files.
• Use PELE to minimize these PDB files.
• RMSD comparison between PELE and QM minimized structures.

If the energetic equation, gradient and hessian of the new dihedrals approach is implemented correctly in PELE, we would expect that its minimized structures do not deviate from the ones used as input coming from QM.

[martimunicoy]

Support

• Example that runs a PELE minimization.

[laumalo]

Implementation

The implementation of the benchmark contemplates two scenarios. Only benchmark ligands with a non null phase constant (filtered structures) or benchmark the whole dataset (all structures) obtained from QCportal.

For only non null phase constant (filtered structures with only non-standard dihedrals):

benchmark = MinimizationBenchmark(
        dataset = 'SMIRNOFF Coverage Set 1',
        out_folder = 'SET1')
benchmark.run(filter_structures = True)

for getting all the structures, the following flag has to be changed:

benchmark.run(filter_structures = False)

• Structural Histogram

To compute the RMSD and obtain an histogram of the results.

benchmark.compute_RMSD()

• Energetic Histogram

To compute the energetic different and obtain an histogram of the results.

benchmark.energetic_difference()

[laumalo]

Results

• Results for the MinimizationBenchmark with the SMIRNOFF Coverage Set.