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Author Topic: Analysis of trajectory from Molecular Dynamics  (Read 208 times)

Offline shvelarde

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Analysis of trajectory from Molecular Dynamics
« on: July 07, 2020, 11:53:48 pm »
Dear Professor Xiang-Jun,

I found this old post (http://forum.x3dna.org/feature-requests/trajectory-over-time/) regarding the analysis of an entire trajectory from MDs.

In that post your response was: 3DNA -- you may want to try the x3dna_ensemble Ruby script...
                                                   using do_x3dna and 
                                                   DSSR -- there is no similar functionality yet

Given that do_x3dna seems to be outdated, I was wondering if still DSSR can not handle entire trajectories from MDs.

Also, I would like to ask, if I have a complete trajectory in some binary format and I convert such trajectory to a pdb file, DSSR would be able to
analyze the trajectory? The web version of DSSR seems to handle trajectories for around 50 frames...


Thanks a lot in advance

S h.v

Offline xiangjun

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Re: Analysis of trajectory from Molecular Dynamics
« Reply #1 on: July 08, 2020, 11:25:57 am »
Hi S h.v,

Thanks for using 3DNA/DSSR, and for posting your questions on the Forum.

Quote
Given that do_x3dna seems to be outdated, I was wondering if still DSSR can not handle entire trajectories from MDs.

Yes, try DSSR with options --md (alias --nmr) and --json.

Quote
Also, I would like to ask, if I have a complete trajectory in some binary format and I convert such trajectory to a pdb file, DSSR would be able to analyze the trajectory? The web version of DSSR seems to handle trajectories for around 50 frames...

DSSR starts from standard PDB or mmCIF format, not any non-standard binary format.

Which web version of DSSR are you referring to? Please be specific.

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

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* Original Poster, please provide a summary
* DSSR 2.0 has superseded the 3DNA v2.4 suite

Offline shvelarde

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Re: Analysis of trajectory from Molecular Dynamics
« Reply #2 on: July 08, 2020, 01:49:47 pm »
Hi Xiang-Jun,

Thanks a lot for your quick response.

I have a molecular dynamics (gromacs) trajectory: name.xtc. I upload this trajectory in vmd,  I removed the water and ions and saved
only 50 frames of the nucleic acids in a pdb format.

Then, I tried:

a) the webserver: http://wdssr.x3dna.org/analyze/. However, I am confused, the obtained results are for the 50 frames or only for the first one? I mean, the results are a statistical average?

b) dssr in the terminal using: x3dna-dssr -i=nuclei_50Frames.pdb --nmr
However I got the following message: no models found: ignoring the --nmr option.
Then, it shows
Processing file 'nucleci_50Frames.pdb',  and then show the results for presumably the first frame.

I suppose that I have an incorrect format in my pdb file. Because, the same command works fine with the included example  of x3dna (old 2.4version)
x3dna-dssr -i=sample_md0.pdb --nmr
However, the results are individual analysis of each frame, right? I mean, the results are not an statistical average?

To be sincere, is the first time that I perform MDs of DNA-B. I am just trying to figure out what physical quantities are more suited to
quantify the deformation of the DNA.

Thanks a lot

Salvador h.v





Offline xiangjun

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Re: Analysis of trajectory from Molecular Dynamics
« Reply #3 on: July 08, 2020, 02:55:19 pm »
Hi Salvador h.v,

Quote
a) the webserver: http://wdssr.x3dna.org/analyze/. However, I am confused, the obtained results are for the 50 frames or only for the first one? I mean, the results are a statistical average?

The http://wdssr.x3dna.org website was developed by Dr. Shuxiang Li, a former postdoc from the Olson lab at Rutgers. Shuxiang has left a while ago for another position. He may chime in to answer your questions, but I am not sure.

Quote
b) dssr in the terminal using: x3dna-dssr -i=nuclei_50Frames.pdb --nmr
However I got the following message: no models found: ignoring the --nmr option.
...

Please attach your nuclei_50Frames.pdb file together with the specific commands and messages. Reproducibility is the KEY.

Quote
To be sincere, is the first time that I perform MDs of DNA-B. I am just trying to figure out what physical quantities are more suited to quantify the deformation of the DNA.

In this case, you may want to first become familiar with well-documented cases in whatever packages you are using. I am not a practitioner of MD simulations, and I cannot provide advices in that filed. If you want to pursue DSSR further, I'd be happy to guide you through any technical aspects.

Xiang-Jun

Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

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* Original Poster, please provide a summary
* DSSR 2.0 has superseded the 3DNA v2.4 suite

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.