Theory:
Dynamical Non-Equilibrium Molecular Dynamics (D-NEMD), to distinguish it from standard NEMD, only used to simulate stationary nonequilibrium states, is based on a generalization of linear response theory.
The idea has been formulated by Onsager in the thirties in metaphysical language; given a solid foundation in the fifties by Green and Kubo (in the linear and nonlinear regime); and adapted to MD simulations by the Giovanni Ciccotti in collaboration with G.Jacucci and I.R.Mac Donald in the seventies.
It has been called the nonlinear Kubo-Onsager relation, connecting dynamical nonequilibrium averages or dynamical relaxations to stationary probability distribution functions (initial distribution) suitably sampled
Ref:
1. Ciccotti, G., Jacucci, G. & McDonald, I.R. Thought-experiments by molecular dynamics. J Stat Phys 220 21, 1-12 (1979)
2.Ciccotti, G. Computer simulation in material science. P. V. Meyer M, Ed. (Kluwer Academic 222 Publishers), 119–137 (1991). 223
3. Ciccotti, G. & Ferrario, M. Non-equilibrium by molecular dynamics: a dynamical approach. Mol Simul 224 42, 1385-1400 (2016). http://dx.doi.org/10.1080/08927022.2015.1121543
From “Structural insights in cell-type specific evolution of intra-host diversity by SARS-CoV-2”
the procedure used to set up and analyze the nonequilibrium MD simulations. From the cryo-138 EM structure of the S proteins with LA bound, three equilibrium MD simulations, 200 ns each, were 139 performed. These equilibrium simulations (indicated by rectangles filled in grey) were used to generate 140 starting conformations for the nonequilibrium simulations (rectangles filled in white).