A mezoscopic model of nucleic acids. Part 1. Lagrangian and quaternion molecular dynamics.
This study presents a model for mezoscopic molecular dynamics simulations with objects of different scale and properties e.e. atoms, pseudoatoms, rigid and pseudo-elastic bodies, described by the external coordinates and internal degrees of freedom. The Lagrangian approach is used to derive equations of motion and a quaternion representation is used for the description of the dynamics of rigid and pseudo-elastic molecular elements. Stability of the LQMD algorithm was tested for a 10-base pair deoxynucleotide. The total energy, momentum and angular momentum are conserved for time-steps up to 20 fs.
Rudnicki
W R
WR
Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Poland. W.Rudnicki@icm.edu.pl
Bakalarski
G
G
Lesyng
B
B
D000465:Algorithms; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D015233:Models, Statistical
D004247:DNA