ABSTRACT
Molecular modeling and computer simulation with empirical
potential energy function (force field) are now routinely carried out
to help understand and predict structures and dynamics of proteins
and other macromolecules of biological relevance in water and
membrane environments. After over 40 years of development, pop-
ular force fields such as AMBER, CHARMM, OPLS and GROMOS have
been widely employed in biomolecular simulations. These force
fields are used dominantly in highly optimized molecular dynamics
simulation packages including AMBER, CHARMM, GROMACS and
NAMD that greatly facilitated molecular dynamics (MD) simulation
of biological molecules. Advance in computer technology, especially
the recent effort in migrating the MD code to graphics processing
unit (GPU) and the emergence of the special-purpose computer
system such as Anton, has extended theMD simulation time tomuch
longer than could be reached just a few years ago.
