NAFlex Simulation Engines

NAFlex offers a variety of simulation tools obtain dynamic information of nucleic acids. Basically the server has two main kind of Simulation Engines:

  • Atomistic Molecular Dynamics Simulations:
    Molecular Dynamics Simulations with fully atomistic representation, in which all atoms (usually including the solvent's) are considered explicitly.

  • Coarse-Grained Simulations:
    Coarse-Grained Simulations, where collections of atoms (number of them depending on the desired resolution) are represented by a few spherical beads connected by springs. NAFlex implements a couple of Coarse-grained algorithms, one at Nucleotide-Base Level (Mesoscopic Elastic Model) and another one at M x Base-Pair Level (Worm-Like Chain Model).

Atomistic MD vs Coarse-Grained

Atomistic Molecular vs Coarse-Grained Representation ( J.Chem.Phys. 126, 2007 )