Open martimunicoy opened 3 years ago
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)
To compute the RMSD and obtain an histogram of the results.
benchmark.compute_RMSD()
To compute the energetic different and obtain an histogram of the results.
benchmark.energetic_difference()
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
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.