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MD simulations


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[1] Analysis of major groove and minor groove

[2] about "curavture" and "tangent" in dnaMD

[3] do_x3dna as a plugin for VMD and update in dnaMD

[4] local helical axis vector for strongly bent DNA

[5] How to analyze helical parameters of DNA with unnatural bases

[6] How to generate a Methylated DNA pdb file from sequence to be use in MD

[7] do_x3dna: a tool to analyze DNA/RNA in molecular dynamics trajectories

[8] Analysis of Amber .mdcrd File

[9] "Ruby in cygwin"


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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.

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