Simulations of the molecular dynamics of nucleic acids

Author(s): Auffinger P, Westhof E


The growing amount of high quality molecular dynamics simulations generated using the latest methodological developments and force fields has led to a sharper understanding of the forces underlying the dynamics of biomolecular systems, as well as to stimulating insights into the structure and catalysis of nucleic acids. It is now clear that inclusion of long-range electrostatic interactions and of the aqueous and ionic environment is necessary for producing realistic and accurate simulations. Yet, many papers hint at a force field and protocol dependence of the results and thus contain the seeds for the future improvements that will be necessary for deepening our understanding of recognition phenomena and folding of nucleic acids.

Similar Articles

GROMACS: fast,flexible, and free

Author(s): Van Der Spoel D,Lindahl E, Hess B, Groenhof G, Mark AE, et al.