How to extract the structures not belonging to the free energy minimum

[satyajitkhatua09]

Dear Users,

I have a general question about extracting the structures from the projected data in the TICs space. I know we can extract the structures from the available meta-stable states. But my query is whether we can extract it from a user-defined free energy range, or is it even possible?

I would appreciate any help you could give me with this.

Thanking you,
Satyajit Khatua

[thempel]

Hi, you can do a clustering in TIC space and extract representative structures from these clusters. Maybe using a regular space clustering is a good choice here, because it will give you better resolution outside of the free energy minima. Once you have done that, you can use the method sample_indexes_by_cluster of the clustering object to obtain frames from your md simulation - write these out in the same way that you normally do with the metastable states. You only need to find a way to figure out which of your cluster centers you want to extract, i.e., which ones are "not in the free energy minimum".