  For many biological applications of molecular dynamics (MD) the importance of
good sampling in conformational space makes it necessary to eliminate the
fastest motions from the system in order to increase the time step. An accurate
knowledge of these motions is a necessary prerequisite for such efforts. It is
known that harmonic vibrations of bond lengths and bond angles produce the
highest frequencies in proteins. There are also fast anharmonic motions, such
as inter-atomic collisions, which are probably most important when bond lengths
and bond angles are fixed. However, the specific time scales corresponding to
all these limitations are not known precisely. In order to clarify the above
issue this paper analyses time step limiting factors in a series of numerical
tests by using an internal coordinate molecular dynamics approach, which allows
chosen internal coordinates to be frozen. It is found that, in proteins, there
is a rather complicated hierarchy of fast motions, with both harmonic and
anharmonic effects mixed together at several close time scales. Non-bonded
interactions, notably strong hydrogen bonding, create locally distributed
normal modes with frequencies similar to those of bond stretching between
non-hydrogen atoms. They also impose ubiquitous anharmonic limitations starting
from rather small step sizes. With fixed standard amino acid geometry,
rotations of hydrogen bonded hydroxyl groups limit time steps at the 5 fsec
level. The next important limitation occurs around 10 fsec and is created by
collisions between non-hydrogen atoms.
