PyEMMA

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Thanks for submitting an issue! Here's a quick checklist in what to include: - [ ] Include a detailed description of the bug or suggestion - [ ] `pip list`...

Chakrabort123

I am using the estimate_umbrella_sampling function with the dtram estimator in order to get an unbiased PMF profile for an umbrella sampling study of membrane permeation. I would like to...

Cal-JWRW

Thanks for developing this module for detecting the MSM states. I am new to PyEMMA. I want to apply this package to understand the metstable states present in my system...

raylab-projects

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

1

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...

satyajitkhatua09

OSError: "Unable to open file (file signature not found)" h5py/_objects.pyx:55 related error

1

I am experiencing the following error while saving cluster/msm etc. Going through the tutorial 04-msm-analysis at ( http://www.emma-project.org/latest/tutorials/notebooks/04-msm-analysis.html) I have attached the output of conda list. (https://github.com/markovmodel/PyEMMA/files/10069918/conda_list.csv) Executed command: cluster.save('nb4.pyemma',...

suniliisc

TICA on backbone atoms

4

Hi, I am trying to do TICA on backbone atoms but I couldn't find the commands for that. Could please tell me how I can do the TICA only on...

qasimpars

I am trying to source/load an existing .xtc file. It gives me RuntimeError: XTC read error: Compressed 3d coordinate. I am trying to compute tICA. With some trajectories, it works...

Harshitasahni

its showing runtime error

1

**The PROBLEM WHICH I FACED** RuntimeError: An attempt has been made to start a new process before the current process has finished its bootstrapping phase. This probably means that you...

Gourav-Chakraborty

Missing dimensions when performing get_output() method

1

I'm using a Jupyer notebook. The system is CentOS Linux 7 and PyEMMA version 2.5.12 (conda list is attached). I'm following the the tutorial listed here (http://www.emma-project.org/latest/tutorials/notebooks/00-pentapeptide-showcase.html) using my own...

meh47336

Few basic questions regarding building MSM using pyemma.

1

I want to understand the how the thermodynamics and kinetics has changed due to ligand binding. So we have performed several short (1 microsecond) MD simulation with and without ligand....

udnenhsirK