MDPropTrack is a Python3 mini-library designed to facilitate quick property extraction from Molecular Dynamics trajectories, time series plotting and assessment of convergence.
Contents:
- What is it convenient for?
- Installation
- Import and use
- Command line tool usage
- Questions and feedback
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Quickly read and plot data from GROMACS edr files.
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Compute and plot properties from trajectories: radius of gyration, RMSD, area per lipid, bilayer thickness, lipid tail order parameter. Configure calculation of custom properties.
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Assess convergence using time series autocorrelation.
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Plot sequential simulation steps together.
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Save and load DataFrames.
Clone this repository to your local system:
git clone git@github.com:Aleksandr-biochem/MDPropTrack.git
# move to repository folder
cd MDPropTrack
To install or update MDPropTrack into your environment use pip:
pip install .
Now you should be able to call the command line tool:
mdpt -h
File requirements.txt lists the exact versions of the dependencies used during development.
# download libraries using pip
pip install -r requirements.txt
# after that run
pip install .
The full potential of MDPropTrack is unlocked, when it's used as a python library. See tutorial.ipynb for all the details. Here is a quick start snippet:
from MDPropTrack.analysis import PropertyAnalyser
# create analyser for your system and get properties from an edr file
pa = PropertyAnalyser(edr='path/to/simulation.edr')
# call the following method to extract properties into DataFrame
pa.extract_properties()
# look at the DataFrame
pa.data
# plot extracted properties as time series
pa.plot()
# or plot autocorrelation to assess convergence
pa.plot(plot_convergence=True)
MDPropTrack is also equipped with a command line tool mdpt that will read your input files and generate a plot for the requested properties. tutorial.ipynb will help you to better understand the mdpt arguments. Examples:
# see help
mdpt -h
# read a edr file and plot a default list of properties
mdpt -e file.edr -o plot.jpg
# read 2 trajectories as inconsequent steps
# calculate backbone RMSD for chain A and Rg for protein
# use time in ps when plotting
mdpt -t file1.xtc,file2.xtc -p file1.tpr -i -tu ps --rg 'protein' --rmsd 'backbone,backbone and chain A' -o plot.jpg
# read edrs and trajectories
# center the DPPC bilayer
# calculate some MARTINI lipid properties with stride 10
# plot convergence of the properties
mdpt -e file1.edr -t file1.xtc,file2.xtc -p file1.tpr --center_group 'DPPC' --step 10 --apl 'name PO4' --thickness 'name PO4' --scc 'name ??A,name ??B' -o plot.jpg --plot_convergence
If you have a question, which does not seem to be answered in this manual or tutorial, or if you want to report an issue, please, do so in the Issues tab at the GitHub page of this repository. Your feedback is very much appreciated!