"Generalized normal coordinates for the vibrational analysis of molecular dynamics simulations."Gerald Mathias, Marcel D. Baer
J. Chem. Theory Comput. 7, 2028–2039 (2011)
The computation of
vibrational spectra via molecular dynamics (MD)
simulations has made lively progress in recent
years. In particular, infrared spectra are accessible employing ab initio MD, for which only the total dipole
moment has to be computed "on the fly" from the
electronic structure along the trajectory.
The analysis of such spectra in terms of the
normal modes of intramolecular motion, however, still poses a challenge to theory.
Here, we present an algorithm to extract such normal modes from MD trajectories by combining
several ideas available in the literature.
The algorithm allows one to compute both
the normal modes and their vibrational bands
without having to rely on an equipartition assumption, which hampered previous methods.
Our analysis is based on a tensorial definition of the vibrational density of states (VDOS),
which spans both the frequency resolved
and auto--correlations of the
molecular degrees of freedom (DOFs).
Generalized normal coordinates are introduced as orthonormal transforms of
mass--weighted coordinates, which
minimize their mutual cross--correlations.
The generalized normal coordinates and their associated normal modes are
iteratively constructed by a minimization scheme
based on the Jacobi diagonalization.
Furthermore, the analysis furnishes mode local temperatures, which
provide not only a measure for the convergence of the
computed intensities, but permit one also to correct these intensities
towards the ensemble limit.
As a first non--trivial test
application we analyze the infrared spectrum
based on ab initio MD,
which is an important building block of
various dye molecules in molecular biology.
BMO authors (in alphabetic order):