Tutorial on msmbuilder

20 Feb, 2019

Tutorial on msmbuilder

Wei WangSlide available: http://chemwwang.people.ust.hk/cgi-bin/songshanhu.php

Outline

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• Prepare the virtual machine and softwares

• Tutorial of msmbuilder

Outline

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• Prepare the virtual machine and softwares• Method 1: download/copy and use TA’s well configured virtual

machine• Method 2: prepare the virtual machine, required softwares

and python packages by yourself

• Tutorial of msmbuilder

Preparing the Linux system and the softwares

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• Method 1 (use the well configured virtual machine by TA)• Download and Install virtualbox on your windows or Mac

(https://www.virtualbox.org)• Download/copy the well configured virtual machine from this website:

• http://chz379.ust.hk/songshanhu/ubuntu14.04.zip• Or ask TA to copy, then extract the zip files

• Click the icon to open the virtual box• Password for the user:111111

• Method 2 (prepare the virual machine and software by yourself)• Install virtualbox, then install ubuntu linux on the virtualbox• Install anaconda3,vmd and required python packages

https://www.virtualbox.org/

http://chz379.ust.hk/songshanhu/ubuntu14.04.zip

Method 2-step1: Install Ubuntu Linux on VirtualBox

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• Follow below link to install the virtual machine on your computer

• https://itsfoss.com/install-linux-in-virtualbox/

• Better to use VirtualBox version > 5.2, Ubuntu version > 14.04

https://mirrors.163.com/ubuntu-releases/14.04/

https://www.virtualbox.org/wiki/Downloads

• Remember to assign >15.0 GB hard disk to your ubuntu system

in the VirtualBox settings

https://itsfoss.com/install-linux-in-virtualbox/

https://mirrors.163.com/ubuntu-releases/14.04/

https://www.virtualbox.org/wiki/Downloads

Method 2-step2: Install anaconda3 and required python packages

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• Open your ubuntu system

• Download anaconda3 in the ubuntu

• https://rrtuaepo.continuum.io/archive/

• Choose “Anaconda3-4.1.0-Linux-x86_64.sh”, click to download

• Install anaconda3 in your terminal

• Go to “Downloads/” folder and type “bash Anaconda3-4.1.0-Linux-x86_64.sh” in the terminal

• Source ~/.bashrc after the installation finishes

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https://rrtuaepo.continuum.io/archive/

Method 2-step2: Install anaconda3 and required python packages

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• msmbuilder (version >3.6), pyemma, matplotlib>2.1.5• Using conda to install those packages in your terminal

• Suggest also Installing vmd in your ubuntu system, for visualizing the structures• Tutorial: https://www.biostars.org/p/196147/

msmbuilder

pyemma

matplotlib

https://www.biostars.org/p/196147/

Outline

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• Tutorial of msmbuilder• General protocol of building MSM• Example on alanine dipeptide• Project: play with Fs peptide

General protocol of building Markov State Model (MSM)

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Input: MD data Output: Metastable statesKinetics…

1.Loading data

2. tICA

3.Splitting

4.Lumping

Building MSM

Download the tutorial file (data & script)

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• Downloading this file (no need to download if use TA’s virtualbox)• http://chz379.ust.hk/songshanhu/http://chz379.ust.hk/songshanhu/songshanhu_tu

torial_msmbuilder_v2.tar.gz

• Open the terminal (Ctrl+Alt+T), extract the tutorial file in ~/Downloads folder

$ cd Downloads/$ tar –zxvf songshanhu_tutorial_msmbuilder_v2.tar.gz

Download the tutorial file (data & script)

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• Go the the folder “songshanhu_tutorial_msmbuilder_v2” to check the files

$ cd songshanhu_tutorial_msmbuilder_v2/$ cd data/;ls$ cd alanine_dipeptide/;ls$ cd ../../analysis/$ cd alanine_dipeptide/;ls

Example on alanine dipeptide: about the data

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• The system is well characterized by two torsion angles

• The Ramachandran plots of the data show three basins

vmd

Example on alanine dipeptide: open the script

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• Go to the folder “songshanhu_tutorial_v2/analysis/alanine_dipeptide/” and open the ipython script “MSM_for_ala2.ipynb”

$ cd ~/Downloads/songshanhu_tutorial_msmbuilder_v2/$ cd analysis/alanine_dipeptide$ jupyter notebook MSM_for_ala2.ipynb

Example on alanine dipeptide: open the script

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• Go to the folder “songshanhu_tutorial_v2/analysis/alanine_dipeptide/” and open the ipython script “MSM_for_ala2.ipynb”

• Then you will see the browser opens a notebook

This notebook contains all the codes needed in the MSM analysis

About Ipython script: how to run the cells

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1. Click and select the cell

2. Click to run the selected cell

3. The results will show here

Example on alanine dipeptide: modules & functions

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• Run the first three cells one by oneDescription of MSM

Loading modules

Loading the functions

Example on alanine dipeptide: inputs

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• Specify the inputs

• Loading the input files

1.Loading data

2. tICA

3.Splitting

4.Lumping

Building MSM

All the results will be shown in the browser & store in the resultdir folder

Example on alanine dipeptide: tICA

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• Code

1.Loading data

2. tICA

3.Splitting

4.Lumping

Building MSM

Compute pairwise distances

Run tICA

Interpret the results


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• Code

• Results

1.Loading data

2. tICA

3.Splitting

4.Lumping

Building MSM


Run tICA


1. Data projected on principal components


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• Code

• Results

1.Loading data

2. tICA

3.Splitting

4.Lumping

Building MSM


Run tICA


(Ctrl+Alt+T) to open a new terminal$ cd results/$ vmd tica-dimension-tIC0.xtc ../trajs/ala2.pdb

Visualizing trajectory using vmd

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1. Click RMSD Trajectory Tool

2. Click RMSD, then Click Align

3. Right click hereClick delete

4. Delete the last frame

(200)5. Click Reset View

6. Click here


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2. Interpret physical meaning of tIC

1.Loading data

2. tICA

3.Splitting

4.Lumping

Building MSM


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• Code

1.Loading data

2. tICA

3.Splitting

4.Lumping

Building MSM

Play with these parameters

Visualize other tICs

1. Data projected on principal components 2. Interpret physical meaning of tIC

Example on alanine dipeptide: Splitting

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• Code

• Output

1.Loading data

2. tICA

3.Splitting

4.Lumping

Building MSM

Play with the number of microstatesClustering into microstates

Visualizing the clusters

Example on alanine dipeptide: Interpret microstate MSM

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• Implied timescale

1.Loading data

2. tICA

3.Splitting

4.Lumping

Building MSM

Play with the range


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1.Loading data

2. tICA

3.Splitting

4.Lumping

Building MSM

Play with the range

1. Gap => The molecule has three metastable states


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1.Loading data

2. tICA

3.Splitting

4.Lumping

Building MSM

Play with the range

1. Gap => The molecule has three metastable states

2. The top two curves reach plateau => Markovian lag time


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• Slowest dynamic modes and corresponding timescale

1.Loading data

2. tICA

3.Splitting

4.Lumping

Building MSM

Markovian lag time (obtained from implied timescale)

Timescale for slowest transition

Visualizing the slowest transition in this system

c.f.


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• Slowest dynamic modes and corresponding timescale

1.Loading data

2. tICA

3.Splitting

4.Lumping

Building MSM

Markovian lag time (obtained from implied timescale)

Timescale for slowest transition

Visualizing the slowest transition in this system

c.f.The slowest transition of this

system is the change of Psi angle


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6. Click here

Example on alanine dipeptide: Lumping

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• Code

1.Loading data

2. tICA

3.Splitting

4.Lumping

Building MSM

Clustering into macrostates



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• Code

1.Loading data

2. tICA

3.Splitting

4.Lumping

Building MSM



Obtained from the implied timescale


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• Code

• Output

1.Loading data

2. tICA

3.Splitting

4.Lumping

Building MSM




c.f.


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• Code

• Output

1.Loading data

2. tICA

3.Splitting

4.Lumping

Building MSM




c.f.

Example on alanine dipeptide: Interpreting macrostates

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• Code

• Output structures: view in vmd

1.Loading data

2. tICA

3.Splitting

4.Lumping

Building MSM

S0

S1

S2

Example on alanine dipeptide: Kinetics & Thermodynamics

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• Obtain Markovian lag time to build the microstate MSM

Output: Metastable statesKinetics…

Markovian lag time


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• Stationary population, Mean first passage time, Kinetic rate, dominant pathways can be obtained


Obtained from the microstate implied timescale


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Slowest216 ps


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Slowest216 ps


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Output: Metastable statesKinetics… Play with the two macrostates you are interested in

S0 S2

S1

Dominant pathway24%

27%49%


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S0 S2

S1

Dominant pathway24%

27%49%

Slowest216 ps

Outline

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• Tutorial of msmbuilder• General protocol of building MSM• Example on alanine dipeptide• Project: play with Fs peptide

data & script

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• Fs peptide dataset

• Fs peptide: contains 21 amino acids

• It’s folding dynamics is complex

script

Play with the script

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• Figure out the physical meaning of the first tIC• Tips: open “tica-dimension-tIC0.xtc” in vmd (remember to align the

structures before visualization

• Figure out the timescale for the slowest transition• Tips: first dynamic mode of the microstate MSM & below two figures

Summary

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Input: MD data Output: Metastable statesKinetics…

1.Loading data

2. tICA

3.Splitting

4.Lumping

Building MSM

Useful websites

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• Vmd: https://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/

• Msmbuilder: http://msmbuilder.org/3.8.0/• PyEMMA: http://emma-project.org/latest/

https://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/

http://msmbuilder.org/3.8.0/

http://emma-project.org/latest/


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6. Click here

Check the ”reference_results” folder

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• This folder contains the standard output for the two examples

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