Tim Hempel

This sort of parameter optimization can be part of the optimization procedure to estimate a valid Markov model. Unfortunately, we cannot help you with that. However, the reason why you...

I'm not really sure if there is a good way of doing it manually. You can of course try to start the HMM optimization from the PCCA memberships estimated at...

The new class is in there. ``` from adaptivemd.mongodb.base import StorableMixin StorableMixin.descendants() ``` ``` [adaptivemd.mongodb.object.ObjectStore, adaptivemd.mongodb.file.DataDict, adaptivemd.file.Location, adaptivemd.file.Action, adaptivemd.generator.TaskGenerator, adaptivemd.task.BaseTask, adaptivemd.brain.Brain, adaptivemd.resource.Resource, adaptivemd.engine.engine.Frame, adaptivemd.engine.engine.OutputTypeDescription, adaptivemd.model.Model, adaptivemd.logentry.LogEntry, adaptivemd.worker.Worker, adaptivemd.mongodb.file.FileStore, adaptivemd.file.File, adaptivemd.file.JSONFile,...

I'm well aware that this is not a just-press-the-button notebook. I tried to set-up and run a minimal example class and script. I started from the first example in notebook...

As you say, it only fails for `mdconvert`. Using `load_dcd` with `save_xtc` works fine, so not a big deal! This is a minimal example that reproduces the problem: ```python import...

Hi, you can do a clustering in TIC space and extract representative structures from these clusters. Maybe using a [regular space clustering](http://www.emma-project.org/latest/api/generated/pyemma.coordinates.clustering.RegularSpaceClustering.html#pyemma.coordinates.clustering.RegularSpaceClustering) is a good choice here, because it will...

TICA reduces dimensions according to a variance cutoff, which defaults 95%. That means 95% of the kinetic variance are kept in the transformed data, which should explain the dimension reduction...

With the output dictionary I just suggested in #23, shouldn't it be possible to call an adaptive simulation by running the pyemma analysis on a specific trajectory type, e.g. `modeller.taks_run_msm_files(list(project.trajectories['protein']),...

You are absolutely right. Paths are now directly passed with file names from `PyEMMAAnalysis` to `_remote`. So far, it seems to work fine.

I agree that these naming conventions are confusing and can be different in different communities. I'd probably stay close to the definitions of amino acid residues given in the major...