Tr. Stouch et al., SUPERCOMPUTING STUDIES OF BIOMEMBRANES, The international journal of supercomputer applications and high performance computing, 8(1), 1994, pp. 6-23
Although computer simulation of biological molecules has seen widespre
ad growth and is widely accepted as an important biochemical tool, it
is hampered by limited computing resources. Biomolecular systems, by n
ecessity, contain a large number of interaction sites, In many cases,
these sites interact over quite large distances. Further, the time sca
les of biological interest are long, which requires that simulations o
f dynamical properties at the atomic level must be lengthy to adequate
ly probe these motions. We address these issues through discussions of
atomic-level molecular dynamics simulations of biological lipid bilay
er membranes, which are key constructs in biochemistry. These simulati
ons reproduce many experimental observables and provide a degree of re
solution currently unavailable experimentally. The lengths of these si
mulations, the longest of which was 2 nanoseconds, were sufficient to
effectively sample many of the motions governing the behavior of biome
mbranes. Examples are given showing the importance of long-range inter
actions. The number of interaction sites required by these simulations
is discussed, particularly the need for explicit representation of so
lvent molecules.