Paper Citing NAMD - Abstract
Voulgarakis, Nikolaos K.; Satish, Siddarth; Chu, Jhih-Wei
Modelling the viscoelasticity and thermal fluctuations of fluids at the nanoscale
MOLECULAR SIMULATION, 36:552-559, 2010
Simulation methodologies for modelling the viscoelasticity and thermal fluctuations of molecular fluids at nanoscale are presented. In particular, we bridge the distinct frameworks of fluctuating hydrodynamics (FHD) and molecular dynamics (MD) simulations using a coarse-graining procedure that properly considers the effective size of each fluid molecule in mapping a phase space vector of the all-atom model to field variables in the FHD representation. We also generalise the FHD equations to model non-Markovian rheological responses by incorporating coloured noise. To capture the increasing elastic responses that emerge at the nanoscale, a composite Newtonian-Maxwell rheological model is developed. Numerical simulations using a staggered discretisation scheme demonstrate that the thermodynamic states and dynamic properties (power spectra) of FHD equations match with those of all-atom MD simulations quantitatively. This agreement also unambiguously determines the wavenumber-dependent transport coefficients of the composite Newtonian-Maxwell model. To avoid the complexities associated with using wavenumber-dependent transport coefficients, we characterise the approximation of using a single set of transport coefficients. We find that for collective fluctuations with a wavelength longer than 25 angstrom, wavenumber-independent models can accurately describe the power spectra. For fluctuations with shorter wavelengths, relative errors in power spectra increase monotonically with wavenumber.
