On the effect of the thermostat in non-equilibrium molecular dynamics simulations

Abstract

The numerical investigation of the statics and dynamics of systems in non-equilibrium in general, and under shear flow in particular, has become more and more common. However, not all the numerical methods developed to simulate equilibrium systems can be successfully adapted to out-of-equilibrium cases. This is especially true for thermostats. Indeed, even though thermostats developed to work under equilibrium conditions sometimes display good agreement with rheology experiments, their performance rapidly degrades beyond weak dissipation and small shear rates. Here we focus on gauging the relative performances of three thermostats, Langevin, dissipative particle dynamics, and Bussi-Donadio-Parrinello under varying parameters and external conditions. We compare their effectiveness by looking at different observables and clearly demonstrate that choosing the right thermostat (and its parameters) requires a careful evaluation of, at least, temperature, density and velocity profiles. We also show that small modifications of the Langevin and DPD thermostats greatly enhance their performance in a wide range of parameters.

Physical Interactions Driving the Activation/Inhibition of Calcium/Calmodulin Dependent Protein Kinase II

“…But this is not a problem in terms of the conclusions we draw, which are based on the internal forces of the system, particularly on electrostatics. Nevertheless, in order to confirm our results, we repeated the simulations using a much softer thermostat, with a coupling constant of 0.2 ps −1 , which is more appropriate for out-of-equilibrium simulations[37] (although temperature could have larger fluctuations). We obtained practically identical results to those in Figure 2, highlighting the robustness of our approach to capture the physical effects on the system.…”

Theoretical insights into C–H bond activation of methane by transition metal clusters: the role of anharmonic effects

“…Ni 4 O 6 (CH 4 ) 2 , that is explicitly stable on including the anharmonic contribution to the free energy, to determine its characteristic vibrational normal modes. For this, we have run 8 ps aiMD simulation in the canonical ensemble with Bussi-Donadio-Parrinello (BDP) 79 thermostat. From Figure 3, we have noticed significant dissimilarities between the harmonic and anharmonic IR spectra of Ni 4 O 6 (CH 4 ) 2 .…”

Tuning the rheological behavior of colloidal gels through competing interactions

“…(1). Affine deformations are considered by acting of the dissipative forces on the peculiar velocity [41,42]…”