Computational protocol: Base Flip in DNA Studied by Molecular Dynamics Simulations of Differently-Oxidized Forms of Methyl-Cytosine

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Protocol publication

[…] All molecular images were generated with VMD (visual molecular dynamics) []. Structural analysis was performed using standard programs; Curve+ [], Gromacs [] tools and home-made scripts. The molecular dynamics simulations have been carried out using the program NAMD2.9 and applying the CHARMM27 force field. Simulations have been performed on the local Linux cluster of the physics department, on the ZEDATuniversity cluster (soroban), and using resources of the North-German Supercomputing Alliance (HLRN). […]

Pipeline specifications

Software tools VMD, GROMACS
Application Protein structure analysis
Chemicals Hydrogen