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MT – I’m implementing the splitting of nonbondedforce into two CustomNonbondedForce and two exceptions (General) Is PME cutoff important? Are there cases where 1-4 distances could span the cutoff so they’d get mangled with exceptions? MT – so cutoffs and 1-4s don't interact with each other in the vast majority of cases. PE – If you’re looking to separate vdW and Electrostatics energies, then having two CustomNonbondedForces, then this is a fine choice
MT – If I ALSO wanted to get 1-4 pair energy for each component, what’s the best way to go? Could I have two exception forces? PE – I think that would work, but I’m not 100% sure. Feel free to test it out and tell me if anything comes up. There may be some interaction between PME and 1-4 interactions, but I think it could be handled right. MT – So this would be a NonbondedForce, CustomNonbondedForce, and two BondForces
MT – I’ve been working on energy equivalence between engines
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MT – How self-consistent are MD engines? PE – A few factors: Things will always be limited by machine precision. Last-digit differences may arise based on the order of adding numbers, which can be effectively random even on the same machine, since the order of operations may affect rounding. Insufficient sampling of energy landscape will lead to differences in outcome
MT – Given a single-point energy evaluation, how reproducible should results be?
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