msmbuilder

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Hi, I am using cartesian featuriser in MSMBuilder on CA atoms using the DESRES dataset. The input looks like following ``` #!/usr/bin/env python #msmbuilder imports from msmbuilder.dataset import dataset from...

sbhakat

Hi, I'm having an issue performing MSM with msmbuilder after I have cropped my simulation from 154352 to 5884 atoms to reduce the complexity of the calculation. When I perform...

girodat

I have read the example of Fs Peptide. tICA function can handle 28 trajectories one time. After featurization and normalization, 28 trajectories formed 28 sub-data. I found I could get...

Juanrong

Apparently, the absolute path of the Travis build is used (`/home/travis/...`) instead of the relative path to the current page. For example, [Fs Peptide (in RAM)](http://msmbuilder.org/development/examples/Fs-Peptide-in-RAM.html) links (in the bottom)...

jaimergp

Hi, I performed the PCCAplus macrostate analysis like following: ``` from msmbuilder.lumping import PCCAPlus pcca = PCCAPlus.from_msm(msm, n_macrostates=5) macro_trajs = pcca.transform(clustered_trajs) ``` Plotting it looks like following  I want...

sbhakat

Hi, Msmbuilder is a great project! I am trying to understand and use it. There is a series of papers on tICA For example, in "tICA-Metadynamics: Accelerating Metadynamics by Using...

DaMaoShan

Some questions about RawPositionsFeaturizer

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I have some queries regarding `RawPositionsFeaturizer` 1. If I want to use atom indices as mentioned in the document like `RawPositionsFeaturizer(atom_indices=None, ref_traj=None)`. Is the following correct way of using it...

sbhakat

I'm trying to find a good lag_time for the MSM by plotting the timescales using: ``` n_clusters = 6 reassignment_ratio = 0.2 tol = 0.5 max_no_improvement = 2000 max_iter =...

orthonalmatrix

Hello! I'm trying to do the MSMBuilder tutorial, but when I type in "TemplateProject", I get the output below: For reference, I managed to install msmbuilder per the installation instructions...

lilianabello

I've been successful at creating the msm and then plotting the free energy landscape with smaller data sets. But once I try to include all my data, I get warning...

orthonalmatrix