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MD simulations

Topics

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[1] generate DNA pdb file for Gromacs

[2] DNA step parameters

[3] Superimpose representative cluster of a RNA strand after simulation

[4] Unnatural base pair helical parameters

[5] Failed Downloading MD Ruby Scripts of 3DNA

[6] Filter frayed ends or broken H bonds

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

[8] Analysis of helical parameter of DNA with unnatural

[9] Analysis of major groove and minor groove

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.