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.
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?
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.
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 .
@@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
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!
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!
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 !
Please go and read the difference between the pdb and psf or have a look at this video ruclips.net/video/qZ85MC4QBAw/видео.html or this ruclips.net/video/ffPnh8wF-ig/видео.html
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?
I have set of PDB files of difference 3D structures of a given peptide sequence. How could I cluster it based on rmsd ?
الاستاذ محمد هل ممكن ان تدلنا عن كيفية إجراء دراسة PCA باستخدام GROMACS. شكرا.
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.
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?
Thank you ! Could you also please do a tutorial to calculate binding energy between two chains during a simulation trajectory ?
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.
Noted
@@Mohamedshehata Thanks!
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.
Thank you so much ! May I ask , is this possible to calculate the pairwise RMSD using GROMACS commands?
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 .
@@lilywang8688 My deepest thanks and gratitude ! :)
Can anyone share how to create free energy landscape using g_sham
Can you please do a PCA calculation/plotting video tutorial using jupyter notebook, that will be a great help, thanks in advance.
I will try to do that in the future
@@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
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!
Thanks Mohamed!
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!
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 !
Firstly, Can i use .pdb file instead of .psf? Secondly How to download .psf file from PDB?
Please go and read the difference between the pdb and psf or have a look at this video
ruclips.net/video/qZ85MC4QBAw/видео.html
or this
ruclips.net/video/ffPnh8wF-ig/видео.html
Thank you, that is a really helpful tutorial video!!! Can I calculate RMSD for a molecular instead of protein?
dumb he did for urea which is not a protein
Yes you can!
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 !
Wonderful explanation, thank you so much for the kind upload
You are welcome !
Thanks
userguide.mdanalysis.org/examples/analysis/alignment_and_rms/pairwise_rmsd.html