Pairwise RMSD analysis of a trajectory by using MDanalysis (Python)

MDAnalysis (mdanalysis.org) is an object-oriented library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. MD simulations of biological molecules have become an important tool to elucidate the relationship between molecular structure and physiological function. Simulations are performed with highly optimized software packages on HPC resources but most codes generate output trajectories in their own formats so that the development of new trajectory analysis algorithms is confined to specific user communities and widespread adoption and further development is delayed.
The MDAnalysis library addresses this problem by abstracting access to the raw simulation data and presenting a uniform object-oriented Python interface to the user. It thus enables users to rapidly write code that is portable and immediately usable in virtually all biomolecular simulation communities. The user interface and modular design work equally well in complex scripted workflows, as foundations for other packages, and for interactive and rapid prototyping work in IPython/Jupyter notebooks, especially together with molecular visualization provided by nglview [1] and time series analysis with pandas [2]. MDAnalysis is written in Python and Cython and uses NumPy arrays for easy interoperability with the wider scientific Python ecosystem. It is widely used and forms the foundation for more specialized biomolecular simulation tools. MDAnalysis is available under the GNU General Public License v2.
[1] github.com/aro...
[2] pandas.pydata.org/

[@arorasakshi1996]

Thank you ! Could you also please do a tutorial to calculate binding energy between two chains during a simulation trajectory ?

[@BasicScienceSeries]

Thank you for the video. Very helpful. Please do series on MD analysis and provide more detailed analysis tool. It will be greaat help! Thanks.

[@Mohamedshehata]

Noted

[@BasicScienceSeries]

@@Mohamedshehata Thanks!

[@nouralnajjarinealumni7089]

Thanks Mohamed!

[@lotfibourougaa6209]

الاستاذ محمد هل ممكن ان تدلنا عن كيفية إجراء دراسة PCA باستخدام GROMACS. شكرا.

[@samvedna6965]

Thank you so much for the tutorial. I was wondering what would be the syntax i were want RMSDs to be compared with respect to time (ns) instead of frames.

[@sinhasuman1944]

Wonderful explanation, thank you so much for the kind upload

[@Mohamedshehata]

You are welcome !

[@irawatiroy9722]

Thank you for this wonderful tutorial. I have a doubt. Suppose, I have, say, 10000 frames and I want to calculate RMSD for each 100th frame. Is there any way to add this constraint in the code?

[@arminsultana501]

Thank you. I did a simulation in Desmond. Could u please tell me how to analyze PCA, and FEL analysis data received from Desmond CMS format?

[@phuochuynh1777]

The Y axis range from 70 to 0 while X axis range from 0 to 70. How can i change Y and X in the same value, like Y from 0 to 70 and X from 0 to 70? Thank u so much.

[@vigneshwarankannan4999]

I have set of PDB files of difference 3D structures of a given peptide sequence. How could I cluster it based on rmsd ?

[@sekekeretsu4172]

Thanks

[@Mohamedshehata]

userguide.mdanalysis.org/examples/analysis/alignment_and_rms/pairwise_rmsd.html

[@sinhasuman1944]

Can you please do a PCA calculation/plotting video tutorial using jupyter notebook, that will be a great help, thanks in advance.

[@Mohamedshehata]

I will try to do that in the future

[@peeleabraham997]

@@Mohamedshehata Dear sir, i would like to organize a international workshop on drug discovery during july 13-17. can you please host the workshop through virtual means sir

[@lilywang8688]

Hi Sinha, the MDAnalysis user guide also has a tutorial on PCA :-) userguide.mdanalysis.org/examples/analysis/reduced_dimensions/pca.html
You can download the notebook here: github.com/MDAnalysis/UserGuide/blob/master/doc/source/examples/analysis/reduced_dimensions/pca.ipynb
Hope it helps -- please let me know if you have any questions!

[@alexou981]

Thank you! THis was so helpful!!! I was just wondering, I have 100,000 frames, the kernel has been running for 2 days, is that expected? Thank you again!

[@Mohamedshehata]

Hi! Yup it is expected and in my case it even dies Look , this analysis is very computationally expensive so either you have two options; 1- use strong computer , 2- decrease the number of frmaes and get rid of non needed atoms in your traj. Do you think 100000 frames is needed ? I don't think so !

[@shengtaoyu1514]

Thank you, that is a really helpful tutorial video!!! Can I calculate RMSD for a molecular instead of protein?

[@amardeepsinha1951]

dumb he did for urea which is not a protein

[@Mohamedshehata]

Yes you can!

[@Mohamedshehata]

you can call people dumb ...btw it was protein not urea !
can I call you dumb now? sure not !
Because we are here to learn !

[@MrThrenorius]

Thank you so much ! May I ask , is this possible to calculate the pairwise RMSD using GROMACS commands?

[@lilywang8688]

Hi Mr Thenorius! Absolutely, simply pass in your first trajectory after -f, and your second trajectory after -f2 . Your reference topology can either be a .tpr file, .gro or .pdb file, or similar. For example:
gmx rms -f trajectory_1.xtc -f2 trajectory_2.xtc -s my_tpr_file.tpr -o pairwise_rmsd.xvg
See the GROMACS manual for more: manual.gromacs.org/current/onlinehelp/gmx-rms.html
You can either visualise .xvg files with the xmgrace software, or delete the first few lines starting with @ or # and simply treat it like a numpy array with np.loadtxt .

[@MrThrenorius]

@@lilywang8688 My deepest thanks and gratitude ! :)

[@rikganguly5886]

Can anyone share how to create free energy landscape using g_sham

[@rajvardhankapshikar1698]

Firstly, Can i use .pdb file instead of .psf? Secondly How to download .psf file from PDB?

[@Mohamedshehata]

Please go and read the difference between the pdb and psf or have a look at this video
th-cam.com/video/qZ85MC4QBAw/w-d-xo.html
or this
th-cam.com/video/ffPnh8wF-ig/w-d-xo.html