# Gmx covar analysis- please help!

**URL:** <https://gromacs.bioexcel.eu/t/gmx-covar-analysis-please-help/1197>\
**Category:** User discussions\
**Created:** [December 4, 2020, 7:11am UTC](https://gromacs.bioexcel.eu/t/gmx-covar-analysis-please-help/1197 "2020-12-04T07:11:20Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Bioinformatician](https://avatars.discourse-cdn.com/v4/letter/b/7ea924/32.png) [@Bioinformatician](https://gromacs.bioexcel.eu/u/Bioinformatician)\
**Post date:** [December 4, 2020, 7:11am UTC](https://gromacs.bioexcel.eu/t/gmx-covar-analysis-please-help/1197/1 "2020-12-04T07:11:20Z")

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GROMACS version:5.0.7  
GROMACS modification: Yes/No  
Hi there,

This is my first time doing a PCA/Covariance analysis of a 20ns Protein-Ligand simulation using gmx covar and gmx anaeig commands from Gromacs. From all the selections that the commands gave, I have chosen backbone. The resulting plots are attached. Plot 1 is eigenvectors vrs eigenvalues and plot2 is the 2d scatter plot. Yellow is my reference and blue and green are my hit molecules.

1. [https://ibb.co/8KQBgTQ](https://ibb.co/8KQBgTQ)
2. [https://ibb.co/JdxJ0jQ](https://ibb.co/JdxJ0jQ)

I read a few research articles and I understood about the scatter plot that my hit molecules are taking up lesser conformational space than reference; which is good. But what does the first plot mean? Like i understand that first few eigen vectors contribute to the change in protein dynamics upon ligand binding, but won’t that be a stabilization effect? i would really appreciate if someone could help me analyse these plots in layman terms.

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**Author:** ![cblau](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/cblau/32/5_2.png) [@cblau](https://gromacs.bioexcel.eu/u/cblau)\
**Post date:** [December 4, 2020, 9:56am UTC](https://gromacs.bioexcel.eu/t/gmx-covar-analysis-please-help/1197/2 "2020-12-04T09:56:25Z")

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Hi,

A good step to start is trying to translate back what you see into a structural change. Try to anlayse what movement the different axis describe - you can identify the frames corresponding to the leftmost and rightmost points in your landscape and have a look what structures they represent.

It might be helpful to have a look at some articles that use PCA to understand how you can interpret the results from this analysis, you can e.g. have a look at this one:

[https://doi.org/10.1006/jmbi.2001.4655](https://doi.org/10.1006/jmbi.2001.4655)

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<div class="post-metadata">

**Author:** ![Bioinformatician](https://avatars.discourse-cdn.com/v4/letter/b/7ea924/32.png) [@Bioinformatician](https://gromacs.bioexcel.eu/u/Bioinformatician)\
**Post date:** [December 4, 2020, 10:56am UTC](https://gromacs.bioexcel.eu/t/gmx-covar-analysis-please-help/1197/3 "2020-12-04T10:56:35Z")

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Thank you @cblau for you reply. i did try to align and superimpose my representative structures but there wasn’t any structural difference per se.