  Conventional molecular dynamics simulations macromolecules require long
computational times because the most interesting motions are very slow compared
with the fast oscillations of bond lengths and bond angles that limit the
integration time step. Simulation of dynamics in the space of internal
coordinates, that is with bond lengths, bond angles and torsions as independent
variables, gives a theoretical possibility to eliminate all uninteresting fast
degrees of freedom from the system. This paper presents a new method for
internal coordinate molecular dynamics simulations of macromolecules. Equations
of motion are derived which are applicable to branched chain molecules with any
number of internal degrees of freedom. Equations use the canonical variables
and they are much simpler than existing analogs. In the numerical tests the
internal coordinate dynamics are compared with the traditional Cartesian
coordinate molecular dynamics in simulations a 56 residue globular protein. It
is shown that the traditional and internal coordinate dynamics require the same
time step size for the same accuracy and that in the standard geometry
approximation of amino acids, that is with fixed bond lengths, bond angles and
rigid aromatic groups, the characteristic step size is 4 fsec, that is two
times higher than with fixed bond lengths only. The step size can be increased
up to 11 fsec when rotation of hydrogen atoms is suppressed.
