ABSTRACT
The use of classical potentials for simulations of chemical and
biochemical systems with molecular dynamics has been a field of
intense research. Currently, it is possible to simulate systems with
millions of atoms and millisecond time scales (Schulten et al., 2008;
Shaw et al., 2010). With exa-scale computing, i.e., 1018 floating point
operations per second (FLOPs), on the horizon it is necessary to
evaluate the performance of the current potentials. Indeed, long-
time biomolecular simulations have revealed some issues already.
For example, Raval et al. carried out a study on 24 proteins (both
homology models and experimental structures) used in recent CASP
competitions involving at least 100 μs MD simulations (Raval et al.,
2012). For most systems, the structures drifted away from the
native state, even when starting from the experimental structure.
Although only two conventional force fields were employed, the
authors concluded that this ismost likely a limitation of the available
point-charge force fields. As simulations on these and longer scales
grow more widespread with improvements in computing power,
node inter-connect, and graphical processing unit (GPU) hardware
(Stone et al., 2007), the accuracy of these classical potentials will be
further tested.
