Constant Temperature Ensemble Research Articles

Application of combined Monte Carlo and molecular dynamics method to simulation of dipalmitoyl phosphatidylcholine lipid bilayer

We describe a new equilibration procedure for the atomic level simulation of a hydrated lipid bilayer. The procedure consists of alternating molecular dynamics trajectory calculations in a constant surface tension and temperature ensemble with configurational bias Monte Carlo moves to different regions of the configuration space of the bilayer, in a constant volume and temperature ensemble. The procedure is described in detail and is applied to a bilayer of 100 molecules of dipalmitoyl phosphatidylcholine (DPPC) and 3205 water molecules. We find that the hybrid simulation procedure enhances the equilibration of the bilayer as measured by the convergence of the area per molecule and the segmental order parameters, as compared with a simulation using only molecular dynamics (MD). Progress toward equilibration is almost three times as fast in CPU time, compared with a purely MD simulation. Equilibration is complete, as judged by the lack of energy drift in three separate 200-ps runs of continuous MD started from different initial states. Results of the simulation are presented and compared with experimental data and with other recent simulations of DPPC. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1153–1164, 1999

Thermodynamic perturbation theory applied to the dipolar heteronuclear dumbbell fluid

The perturbation theory of Stell and coworkers as extended by Boublík and Vega is applied to the dipolar heteronuclear dumbbell fluid using the hard heteronuclear dumbbell fluid as a reference system. Monte Carlo simulations in the constant pressure and temperature ensemble have been carried out to determine the accuracy of the theory. The calculated thermodynamic properties are density, internal energy, and chemical potential. The theory shows good agreement with the simulation results over a large range of densities and dipole moments, similar to the findings of Patey and Valleau for dipolar hard spheres.

Thermodynamic perturbation theory applied to the dipolar heteronuclear dumbbell fluid

The perturbation theory of Stell and coworkers as extended by Boublík and Vega is applied to the dipolar heteronuclear dumbbell fluid using the hard heteronuclear dumbbell fluid as a reference system. Monte Carlo simulations in the constant pressure and temperature ensemble have been carried out to determine the accuracy of the theory. The calculated thermodynamic properties are density, internal energy, and chemical potential. The theory shows good agreement with the simulation results over a large range of densities and dipole moments, similar to the findings of Patey and Valleau for dipolar hard spheres.

Off-lattice NPT simulations of spherocylinder fluids

Thermodynamic properties of spherocylinder fluids in the absence of attractive interactions with length to diameter ratio of up to 15 have been determined by computer simulation. Properties that were studied include the isotropic-nematic transition, equation of state, and chemical potential. A constant temperature and pressure ensemble was used in the simulations. The spherocylinders were constrained to lie in one of three mutually perpendicular directions in continuous space. Good agreement was obtained between the computed thermodynamic properties and those predicted by scaled particle theory.

Effect of gas impurity and ion bombardment on stresses in sputter-deposited thin films: A molecular-dynamics approach

Intrinsic stresses in sputter-deposited thin films are studied via a two-dimensional molecular-dynamics model. Two-body potential functions, periodic boundary conditions, and a generalized Langevin equation are applied to determine the microstructure of the film. The intrinsic stresses are then calculated using a stress method. 12 layers of substrate atoms are arranged in the (111) plane at the beginning of the film growth simulation. The molecular-dynamics simulations using the constant pressure and constant temperature ensemble are first carried out to obtain the zero stress state of the substrate. A thin film of Ni atoms is deposited in the presence of a background of argon and energetic ions in order to obtain a reasonable representation of the film structure. After the deposition process is completed, the film and the substrate are allowed to contract or expand in accordance with the elastic energies. It is found that the microstructure and intrinsic stresses of the film depend upon the incident energy of incoming particles, the ion bombardment, and the amount of trapped gas impurity. The model strongly suggests that the argon impurities trapped into the deposited film are the primary cause of the state of compressive stress. It also shows that in sputter-deposited films the magnitude of the compressive stress depends more strongly on the film structure than on the quantity of the argon gas trapped in the film. A tight packing of film atoms around argon atoms is likely to lead to higher compressive stresses in the film.

Thermal shape fluctuations at constant energy

The constant energy ensemble is used to calculate statistical shape fluctuations in hot rotating nuclei. Comparisons are made with the constant temperature ensemble.

A comparison of constant energy, constant temperature and constant pressure ensembles in molecular dynamics simulations of atomic liquids

Dynamic and static properties of the LJ fluid at a density and temperature close to the triple point are determined and compared for molecular dynamics computer simulations using (N, V, E), (N, V, T), (N, P, H) and (N, P, T) ensembles. As expected, the mean values of thermodynamic properties for all the different ensembles show good agreement. For the velocity autocorrelation function and the time dependence of the mean square displacement it is shown that the constant temperature and/or constant pressure algorithms used produce results which are identical, within statistical accuracy, to those obtained using the constant energy ensemble. The equations of motion are presented in a readily implementable form.

Molecular dynamics: conductivity of a fused salt

The electrical conductivity of a model of liquid KCl was determined by molecular dynamics computations. In a constant temperature ensemble, the linear regime for Ohm's law was shown to extend up to at least 1.5 × 10 7 V/cm. The results compared favorably with that calculated by monitoring the power dissipation and with the zero-field value obtained via the current autocorrelation function.