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molecular dynamic Simulation of DNA Polymer

Ali Al-Najada
Department of Chemical & Biomolecular Engineering, University of Tennessee

Presented here is an oxDNA2 model with 100 atmos with an applied pulling force. The model was built in previous work and thier python tool was used to generate lammps configuration files (Coarse-grained simulation of DNA using LAMMPS).

Coarse-Grained DNA model (oxDNA) has been simulated and calculation of the kinetic, rotation, potential energies were performed. Total energy is the sum of the all energies. The DNA model has been simulated with 100 atoms (50 each strand). The system was tested with an increase in the temperature as well as with a pulling force (shown here).1

Interactive Structures

Color Legend:

  • Pale Blue = A nucleotide
  • Gray = T nucleotide
  • Brown = G nucleotide
  • Green = C nucleotide


1. Henrich, O., Gutierrez Fosado, Y. A., Curk, T., & Ouldridge, T. E. (2018). Coarse-grained simulation of DNA using LAMMPS : An implementation of the oxDNA model and its applications. Eur Phys J E Soft Matter, 41(5), 57. doi:10.1140/epje/i2018-11669-8

posted: May 2022.
updated: May 2022.