DD – So increasing the density of the network wouldn’t help, because the individual edges are too noisy?
IA – Too early to say.
JC – I wonder about running edges in two directions, and giving our analysis the option of rejecting simulations.
IA – So the question is: If we have some redundancy, should we plan to allow the anlysis to throw out some edges?
IP – One of the conclusions from Ken’s simulations (which don’t have redundancy, chosen to have the smallest chemical changes), he still needed 20ns for some edges to converge.
JC – But we may need to look closer at those conclusions.
DD – This sounds like the concept of Alchemiscale “strategies”, where something watches the state of the whole network and chooses to kick off new simulations.
IA + RG – We’d love to do this, but need to talk to board about prioritizing this.
IA – Don’t think this is a cinnabar thing…
JC – We could consider a few paths - replicate edges until there’s some sort of agreement, or run lots of stuff and remove edges at analysis-time if they look bad, or dynamically make new edges during the run.
DD – Could trial this on the ASAP side.
JC – Could be handy to have a minimum and maximum time for each edge.
DD – This could be something like a strategy for alchemiscale.
IA – OpenFE will need to talk to its board about initiating this effort. We’re running with triplicates now so we can simulate the effect of this.
JC – We should implement extension first.
IA – Yeah, more technical work needed.
JC – One way we’d thought about this, which might not be the best way, would be to have the hdf5 sitting around for later analysis. But it may be better to
DD – Could make this a recurring agenda item - “implements extends support”, since I agree that would be the first step.
JW – I wouldn’t want this working group to rush ahead with a fix for this if OpenFE
JC – But current results are pretty bad.
IA – I’ve agreed to benchmark nagl. So we want to run larger networks with current PLB. I think we need to brute-force a solution quickly to complete this testing.
JC – Seems like it would be good to run more edges now and be prepared to throw some out. Then you could run statistical tests to see whether edges are converged/totally discordant.
JW – To be clear, I’d like to make sure that us implementing some sort of extends support doesn’t impose costs/complications on OpenFE’s longer term plans to do something similar.