Up: Dynamic and Stochastic Protein
Newton Euler Inverse Mass Operator (NEIMO) Dynamics of Polypeptides
Newton-Euler Inverse Mass Operator (NEIMO) Dynamics is a fast method
for calculating internal-coordinate molecular dynamics. Unlike other
exact methods for solving these equations of motion, computational
time for the NEIMO method is proportional to , rather than
, where is the number of degrees of freedom.
This allows internal-coordinate dynamics to be solved for very large
systems. The first use of the NEIMO method for molecular dynamics is
presented here. Results are given for simulations of a wide range of
peptide and protein systems. The computational time is shown to be
rigorously proportional to . Additionally, the dynamics are
shown to be accurate for timesteps much larger than those used in
Cartesian-coordinate dynamics. For small peptides, timesteps as large
as 20 fs are achievable.