Question:How to remove disconnected microstates in MSMbuilder?

[zhoushuangyan]

Hi all: I want to use MSMBuilder2.8.2 to construct a Markov state model to study the protein folding with 150 discrete trajectroy. After the cluster step with hybrid method,I got the Assignments.h5 and Gens.h5 as well. And then I used this to calculate relaxation timescales,but the lag time did not convergence very well(the total simulation time was 4 microsecond in total). So I think that the disconnect mircrostates may affect this. I tried to use the msmb -h command to find a way to achieve this,and found that TrimAssignments maybe the solution.But I am not sure if this was correct? By the way I am also confused with how to read the data in .h5 files? Or do I need to write a script to convert to .h5 (such as Gens.h5) .dat file?