Title: Virtual Molecular Dynamics,
Abstract: Molecular dynamics is based on solving Newton's equations for many-particle
systems that evolve along complex, highly fluctuating trajectories. The orbital
instability and short-time complexity of Newtonian orbits is in sharp contrast
to the more coherent behavior of collective modes such as density profiles. The
notion of virtual molecular dynamics is introduced here based on temporal
coarse-graining via Pade approximants and the Ito formula for stochastic
processes. It is demonstrated that this framework leads to significant
efficiency over traditional molecular dynamics and avoids the need to introduce
coarse-grained variables and phenomenological equations for their evolution. In
this framework, an all-atom trajectory is represented by a Markov chain of
virtual atomic states at a discrete sequence of timesteps, transitions between
which are determined by an integration of conventional molecular dynamics with
Pade approximants and a microstate energy annealing methodology. The latter is
achieved by a conventional and an MD NVE energy minimization schemes. This
multiscale framework is demonstrated for a pertussis toxin subunit undergoing a
structural transition, a T=1 capsid-like structure of HPV16 L1 protein, and two
coalescing argon droplets.