chrisiacovella
commented
7 years ago Good idea. As Andrew and I just discovered, forcefield size seems to play a significant role as the system size increases.
As we've discussed before, we should have a "reduce" function that outputs just the relevant parameters/rules used for a given system (into an xml file). This would be useful for:
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Publishing papers, as it allows just the parameters used in a paper to be provided
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Speeding up large systems, as you could run the "reduce" function on a small system, then use that forcefield file for the larger system.
To better understand how atomtyping can be sped up, we should create some benchmarks. Some variables that would be worth exploring
System size: scaling from a few hundred or thousand to hundreds of thousands or millions of atoms
Force field size, i.e. an xml file that only contains tip3p water vs. the entire OPLS force field
Sparse vs. dense bond networks, i.e. water vs a slab of hexa-coordinated atoms in a crystal
Might be better to store this code elsewhere & I can contribute some systems