Abstract
Although computer simulation of biological molecules has seen widespread growth and is widely accepted as an important biochemical tool, it is hampered by lim ited computing resources. Biomolecular systems, by necessity, contain a large number of interaction sites. In many cases, these sites interact over quite large dis tances. Further, the time scales of biological interest are long, which requires that simulations of dynamical properties at the atomic level must be lengthy to ade quately probe these motions. We address these issues through discussions of atomic-level molecular dynam ics simulations of biological lipid bilayer membranes, which are key constructs in biochemistry. These simu lations reproduce many experimental observables and provide a degree of resolution currently unavailable experimentally. The lengths of these simulations, the longest of which was 2 nanoseconds, were sufficient to effectively sample many of the motions governing the behavior of biomembranes. Examples are given showing the importance of long-range interactions. The number of interaction sites required by these sim ulations is discussed, particularly the need for explicit representation of solvent molecules.
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
More From: The International Journal of Supercomputer Applications and High Performance Computing
Disclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.