David L. Mobley

Additional things which were discussed on today's call that we will need: - `siblingShuffle( args )` - propose shuffling the order of siblings (with no descendants) within the hierarchy -...

@jchodera , input on this?

@jchodera - I think I agree with the basic "main activities" you summarize, and what those would involve. ## So we would need to implement: - Pick a parameter, possibly...

@jchodera - one other question. I'm not an expert on Metropolis-Hastings yet, but it looks to me like you swapped your proposal probabilities above. Specifically, you say that for adding...

That makes sense. It's where I ultimately ended up, though it wasn't what I got when I first read your note. Thanks for the clarification.

`id` and `parent_id` were added in a recent PR. The other changes will still be needed.

FTR, I believe when we discussed this with Christopher, he indicated that: - it is surprisingly difficult/subtle to do this generally and well in an automated manner - OpenEye is...

I thought our goal at this point was "working small molecule forcefield"? I don't understand why we need to be thinking about larger molecules yet. Can you explain?

I agree that we have to deal with this, and no one's suggesting that we not do anything about it. The question is, "when?" My worry is just that if...

I don't have enough experience with this to be able to comment. mdtraj may be a good model. DM On Mon, Jul 4, 2016 at 6:51 PM, John Chodera [email protected]...