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Questions and answers => MD simulations => Topic started by: xroxzero on November 08, 2017, 11:14:05 am

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Title: about "curavture" and "tangent" in dnaMD
Post by: xroxzero on November 08, 2017, 11:14:05 am
Hello,

I have a question about the unit of "curavture" and "tangent" in dnaMD. 

In dnaMD, my dna contains 24bp, and I type " dnaMD vsTime -i 24bp_dna.h5 -tbp 24 -bs 1 -be 24 -p "curvature" -mm sum -o curvature.dat ".

An error occur, "The requested end bp 24 is out side of 1-23 range" , why the range is 1-23?

This error occur on "tangent" ,too.

Also,I concern the unit of "curavture" and "tangent" ?



Thank you very much for your help,
Anderson
Title: Re: about "curavture" and "tangent" in dnaMD
Post by: Rajendra Kumar on November 08, 2017, 12:02:40 pm
Hi,

As written in tutorial (http://do-x3dna.readthedocs.io/en/latest/notebooks/helical_axis_tutorial.html), axis coordinate is determined using two base-pairs (one base-step) by 3DNA. Therefore, number of helical-axis coordinates is less than one of total number of base-pairs.

Unit of helical-axis is A, therefore, curvature unit is (1/A). Tangents are a list of vectors with same as helical-axis unit.

With regards,
Rajendra

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.