Recovering the Crooks equation for dynamical systems in the isothermal-isobaric ensemble: a strategy based on the equations of motion

The Crooks equation [Eq. (10) in J. Stat. Phys. 90, 1481 (1998)] relates the work done on a system during a nonequilibrium transformation to the free energy difference between the final and the initial state of the transformation. Recently, the authors have derived the Crooks equation for systems in the canonical ensemble thermostatted by the Nose-Hoover or Nose-Hoover chain method [P. Procacci et al., J. Chem. Phys. 125, 164101 (2006)]. That proof is essentially based on the fluctuation theorem by Evans and Searles [Adv. Phys. 51, 1529 (2002)] and on the equations of motion. Following an analogous approach, the authors derive here the Crooks equation in the context of molecular dynamics simulations of systems in the isothermal-isobaric (NPT) ensemble, whose dynamics is regulated by the Martyna-Tobias-Klein algorithm [J. Chem. Phys. 101, 4177 (1994)]. Their present derivation of the Crooks equation correlates to the demonstration of the Jarzynski identity for NPT systems recently proposed by Cuendet [J. Chem. Phys. 125, 144109 (2006)].     

The Jarzynski identity derived from general Hamiltonian or non-Hamiltonian dynamics reproducing NVT or NPT ensembles

The Jarzynski identity (JI) relates nonequilibrium work averages to thermodynamic free energy differences. It was shown in a recent contribution [M. A. Cuendet, Phys. Rev. Lett. 96, 120602 (2006)] that the JI can, in particular, be derived directly from the Nose-Hoover thermostated dynamics. This statistical mechanical derivation is particularly relevant in the framework of molecular dynamics simulation, because it is based solely on the equations of motion considered and is free of any additional assumptions on system size or bath coupling. Here, this result is generalized to a variety of dynamics, along two directions. On the one hand, specific improved thermostating schemes used in practical applications are treated. These include Nose-Hoover chains, higher moment thermostats, as well as an isothermal-isobaric scheme yielding the JI in the NPT ensemble. On the other hand, the theoretical generality of the new derivation is explored. Generic dynamics with arbitrary coupling terms and an arbitrary number of thermostating variables, both non-Hamiltonian and Hamiltonian, are shown to imply the JI. In particular, a nonautonomous formulation of the generalized Nose-Poincare thermostat is proposed. Finally, general conditions required for the JI derivation are briefly discussed.     

Configurational constant pressure molecular dynamics

We propose two new algorithms for generating isothermal-isobaric molecular dynamics. The algorithms are based on an extended phase space dynamics where two extra degrees of freedom, representing the thermostat and the barostat, are included. These new methods adopt a totally different approach towards molecular dynamics simulation in the isothermal-isobaric ensemble. They are fully configurational in the sense that only the particle positions are required in the control of the system temperature and pressure. Following on from the works of Delhommelle and Evans [Mol. Phys., 99, 1825 (2001)] and of Braga and Travis [J. Chem. Phys., 123, 134101 (2005)] concerning configurational canonical dynamics, these new algorithms can be seen as a natural extension to the isothermal-isobaric ensemble. We have validated both of our new configurational isothermal-isobaric schemes by conducting molecular dynamics simulations of a Lennard-Jones fluid and comparing the static and dynamic properties for a single state point. We find that both schemes generate similar results compared with schemes which use kinetic temperature and pressure control. We have also monitored the response of the system to a series of isothermal compressions and isobaric quenches. We find that the configurational schemes performed at least as well as the kinetic based scheme in bringing the system temperature and pressure into line with the set point values of these variables. These new methods will potentially play a significant role in simulations where the calculation of the kinetic temperature and pressure can be problematic. A well known example resides in the field of nonequilibrium simulations where the kinetic temperature and pressure require a knowledge of the streaming velocity of the fluid in order to calculate the true peculiar velocities (or momenta) that enter into their definitions. These are completely avoided by using our configurational thermostats and barostats, since these are independent of momenta. By extending the analysis of Kusnezov et al. [Ann. Phys., 204, 155 (1990)] in order to derive a set of generalized Nose-Hoover equations of motion which can generate isothermal-isobaric dynamics in a number of different ways, we are able to show that both of our new configurational barostats and Hoover's kinetic isothermal-isobaric scheme are special cases of this more general set of equations. This generalization can be very powerful in generating constant pressure dynamics for a variety of systems.     

Non-Hamiltonian molecular dynamics implementation of the Gibbs ensemble method. I. Algorithm

In this paper (paper I) and the following paper (paper II) [C. Bratschi, H. Huber, and D. J. Searles, J. Chem. Phys. 126, 164105 (2007)], a new molecular dynamics algorithm implementing the Gibbs ensemble will be presented and then on applied to the liquid-vapor coexistence curve for two ab initio CO2 potentials. In paper I, the Gibbs ensemble molecular dynamics algorithm using non-Hamiltonian molecular dynamics techniques is introduced. It is shown that states of the correct probability density function are sampled and the correct exchange probability is generated. The extended system Nose-Hoover formalism is used to generate a constant temperature ensemble with equal pressures in the subsystems, combined with single particle transfers between the subsystems, over several time steps, to get equal chemical potentials.     

Nonequilibrium molecular dynamics of the rheological and structural properties of linear and branched molecules. Simple shear and poiseuille flows; instabilities and slip

Nonequilibrium molecular-dynamics simulations are performed for linear and branched chain molecules to study their rheological and structural properties under simple shear and Poiseuille flows. Molecules are described by a spring-monomer model with a given intermolecular potential. The equations of motion are solved for shear and Poiseuille flows with Lees and Edward's [A. W. Lees and S. F. Edwards, J. Phys. C 5, 1921 (1972)] periodic boundary conditions. A multiple time-scale algorithm extended to nonequilibrium situations is used as the integration method, and the simulations are performed at constant temperature using Nose-Hoover [S. Nose, J. Chem. Phys. 81, 511 (1984)] dynamics. In simple shear, molecules with flow-induced ellipsoidal shape, having significant segment concentrations along the gradient and neutral directions, exhibit substantial flow resistance. Linear molecules have larger zero-shear-rate viscosity than that of branched molecules, however, this behavior reverses as the shear rate is increased. The relaxation time of the molecules is associated with segment concentrations directed along the gradient and neutral directions, and hence it depends on structure and molecular weight. The results of this study are in qualitative agreement with other simulation studies and with experimental data. The pressure (Poiseuille) flow is induced by an external force F(e) simulated by confining the molecules in the region between surfaces which have attractive forces. Conditions at the boundary strongly influence the type of the slip flow predicted. A parabolic velocity profile with apparent slip on the wall is predicted under weakly attractive wall conditions, independent of molecular structure. In the case of strongly attractive walls, a layer of adhered molecules to the wall produces an abrupt distortion of the velocity profile which leads to slip between fluid layers with magnitude that depends on the molecular structure. Finally, the molecular deformation under flow depends on the attractive force of the wall, in such a way that molecules are highly deformed in the case of strong attracting walls.     

A semiclassical hybrid approach to many particle quantum dynamics

We analytically derive a correlated approach for a mixed semiclassical many particle dynamics, treating a fraction of the degrees of freedom by the multitrajectory semiclassical initial value method of Herman and Kluk [Chem. Phys. 91, 27 (1984)] while approximately treating the dynamics of the remaining degrees of freedom with fixed initial phase space variables, analogously to the thawed Gaussian wave packet dynamics of Heller [J. Chem. Phys. 62, 1544 (1975)]. A first application of this hybrid approach to the well studied Secrest-Johnson [J. Chem. Phys. 45, 4556 (1966)] model of atom-diatomic collisions is promising. Results close to the quantum ones for correlation functions as well as scattering probabilities could be gained with considerably reduced numerical effort as compared to the full semiclassical Herman-Kluk approach. Furthermore, the harmonic nature of the different degrees of freedom can be determined a posteriori by comparing results with and without the additional approximation.     

Influence of thermostats and carrier gas on simulations of nucleation

We investigate the influence of carrier gas and thermostat on molecular dynamics (MD) simulations of nucleation. The task of keeping the temperature constant in MD simulations is not trivial and an inefficient thermalization may have a strong influence on the results. Different thermostating mechanisms have been proposed and used in the past. In particular, we analyze the efficiency of velocity rescaling, Nose-Hoover, and a carrier gas (mimicking the experimental situation) by extensive MD simulations. Since nucleation is highly sensitive to temperature, one would expect that small variations in temperature might lead to differences in nucleation rates of up to several orders of magnitude. Surprisingly, the results indicate that the choice of the thermostating method in a simulation does not have--at least in the case of Lennard-Jones argon--a very significant influence on the nucleation rate. These findings are interpreted in the context of the classical theory of Feder et al. [Adv. Phys. 15, 111 (1966)] by analyzing the temperature distribution of the nucleating clusters. We find that the distribution of cluster temperatures is non-Gaussian and that subcritically sized clusters are colder while postcritically sized clusters are warmer than the bath temperature. However, the average temperature of all clusters is found to be always higher than the bath temperature.     

An algorithm for the uniform sampling of iso-energy surfaces and for the calculation of microcanonical averages

In this article an algorithm is proposed to efficiently perform the uniform sampling of an iso-energy surface corresponding to a fixed potential energy U of a molecular system, and for calculating averages of certain quantities over microstates having this energy (microcanonical averages). The developed sampling technique is based upon the combination of a recently proposed method for performing constant potential energy molecular dynamics simulations [Rapallo, A. J Chem Phys 2004, 121, 4033] with well-established thermostatting techniques used in the framework of standard molecular dynamics simulations, such as the Andersen thermostat, and the Nose-Hoover chain thermostat. The proposed strategy leads to very accurate and drift-free potential energy conservation during the whole sampling process, and, very important, specially when dealing with high-dimensional or complicated potential functions, it does not require the calculation of the potential energy function hessian. The technique proved to be very reliable for sampling both low- and high-dimensional surfaces.     

Long-time and unitary properties of semiclassical initial value representations

We numerically compare the semiclassical "frozen Gaussian" Herman-Kluk propagator [Chem. Phys. 91, 27 (1984)] and the "thawed Gaussian" propagator put forward recently by Baranger et al. [J. Phys. A 34, 7227 (2001)] by studying the quantum dynamics in some nonlinear one-dimensional potentials. The reasons for the lack of long-time accuracy and norm conservation in the latter method are uncovered. We amend the thawed Gaussian propagator with a global harmonic approximation for the stability of the trajectories and demonstrate that this revised propagator is a true alternative to the Herman-Kluk propagator with similar accuracy.     

Gradient symplectic algorithms for solving the radial Schrodinger equation

The radial Schrodinger equation for a spherically symmetric potential can be regarded as a one-dimensional classical harmonic oscillator with a time-dependent spring constant. For solving classical dynamics problems, symplectic integrators are well known for their excellent conservation properties. The class of gradient symplectic algorithms is particularly suited for solving harmonic-oscillator dynamics. By use of Suzuki's rule [Proc. Jpn. Acad., Ser. B: Phys. Biol. Sci. 69, 161 (1993)] for decomposing time-ordered operators, these algorithms can be easily applied to the Schrodinger equation. We demonstrate the power of this class of gradient algorithms by solving the spectrum of highly singular radial potentials using Killingbeck's method [J. Phys. A 18, 245 (1985)] of backward Newton-Ralphson iterations.     

The role of exchange-correlation functionals in the potential energy surface and dynamics of N(2) dissociation on W surfaces

We study the dissociative adsorption of N(2) on W(100) and W(110) by means of density functional theory and classical dynamics. Working with a full six-dimensional adiabatic potential energy surface (PES), we find that the theoretical results of the dynamical problem strongly depend on the choice of approximate exchange-correlation functional for the determination of the PES. We consider the Perdew-Wang-91 [Perdew et al., Phys. Rev. B 46, 6671 (1992)] and Perdew-Burke-Ernzerhof (RPBE) [Hammer et al., Phys. Rev. B 59, 7413 (1999)] functionals and carry out a systematic comparison between the dynamics determined by the respective PESs. Even though it has been shown in earlier works that the RPBE may provide better values for the chemisorption energies, our study brings evidence that it gives rise to a PES with excessive repulsion far from the surface.     

Thermodynamical and structural properties of imidazolium based ionic liquids from molecular simulation

We have performed molecular dynamics simulations to determine the densities and heat of vaporization as well as structural information for the 1-alkyl-3-methyl-imidazolium based ionic liquids [amim][Cl] and [amim][BF(4)] in the temperature range from 298 to 363 K. In this simulation study, we used an united atom model of Liu et al. [Phys. Chem. Chem. Phys. 8, 1096 (2006)] for the [emim(+)] and [bmim(+)] cations, which we have extended for simulation in [hmim]-ILs and combined with parameters of Canongia Lopes et al. [J. Phys. Chem. B 108, 2038 (2004)] for the [Cl(-)] anion. Our simulation results prove that both the original united atoms approach by Liu et al. and our extension yield reasonable predictions for the ionic liquid with a considerably reduced computational expense than that required for all atoms models. Radial distribution functions and spatial distribution functions where employed to analyze the local structure of this ionic liquid, and in which way it is influenced by the type of the anion, the size of the cation, and the temperature. Our simulations give evidence for the occurrence of tail aggregations in these ionic liquids with increasing length of the side chain and also increasing temperature.     

Molecular dynamics in the isothermal-isobaric ensemble: the requirement of a "shell" molecule. III. Discontinuous potentials

Based on the approach of Gruhn and Monson [Phys. Rev. E 63, 061106 (2001)], we present a new method for deriving the collisions dynamics for particles that interact via discontinuous potentials. By invoking the conservation of the extended Hamiltonian, we generate molecular dynamics (MD) algorithms for simulating the hard-sphere and square-well fluids within the isothermal-isobaric (NpT) ensemble. Consistent with the recent rigorous reformulation of the NpT ensemble partition function, the equations of motion impose a constant external pressure via the introduction of a shell particle of known mass [M. J. Uline and D. S. Corti, J. Chem. Phys. 123, 164101 (2005); 123, 164102 (2005)], which serves to define uniquely the volume of the system. The particles are also connected to a temperature reservoir through the use of a chain of Nose-Hoover thermostats, the properties of which are not affected by a hard-sphere or square-well collision. By using the Liouville operator formalism and the Trotter expansion theorem to integrate the equations of motion, the update of the thermostat variables can be decoupled from the update of the positions of the particles and the momentum changes upon a collision. Hence, once the appropriate collision dynamics for the isobaric-isenthalpic (NpH) equations of motion is known, the adaptation of the algorithm to the NpT ensemble is straightforward. Results of MD simulations for the pure component square-well fluid are presented and serve to validate our algorithm. Finally, since the mass of the shell particle is known, the system itself, and not a piston of arbitrary mass, controls the time scales for internal pressure and volume fluctuations. We therefore consider the influence of the shell particle algorithm on the dynamics of the square-well fluid.     

Understanding Molecular Dynamics with Stochastic Processes via Real or Virtual Dynamics

Molecular dynamics with the stochastic process provides a convenient way to compute structural and thermodynamic properties of chemical, biological, and materials systems. It is demonstrated that the virtual dynamics case that we proposed for the Langevin equation[J. Chem. Phys. 147 , 184104 (2017)] in principle exists in other types of stochastic thermostats as well. The recommended "middle" scheme[J. Chem. Phys. 147 , 034109 (2017)] of the Andersen thermostat is investigated as an example. As shown by both analytic and numerical results, while the real and virtual dynamics cases approach the same plateau of the characteristic correlation time in the high collision frequency limit, the accuracy and efficiency of sampling are relatively insensitive to the value of the collision frequency in a broad range. After we compare the behaviors of the Andersen thermostat to those of Langevin dynamics, a heuristic schematic representation is proposed for understanding efficient stochastic thermostatting processes with molecular dynamics.     

A molecular dynamics study of water nucleation using the TIP4P/2005 model

Extensive molecular dynamics simulations were conducted using the TIP4P/2005 water model of Abascal and Vega [J. Chem. Phys. 123, 234505 (2005)] to investigate its condensation from supersaturated vapor to liquid at 330 K. The mean first passage time method [J. Wedekind, R. Strey, and D. Reguera, J. Chem. Phys. 126, 134103 (2007); L. S. Bartell and D. T. Wu, 125, 194503 (2006)] was used to analyze the influence of finite size effects, thermostats, and charged species on the nucleation dynamics. We find that the Nose?-Hoover thermostat and the one proposed by Bussi et al. [J. Chem. Phys. 126, 014101 (2007)] give essentially the same averages. We identify the maximum thermostat coupling time to guarantee proper thermostating for these simulations. The presence of charged species has a dramatic impact on the dynamics, inducing a marked change towards a pure growth regime, which highlights the importance of ions in the formation of liquid droplets in the atmosphere. It was found a small but noticeable sign preference at intermediate cluster sizes (between 5 and 30 water molecules) corresponding mostly to the formation of the second solvation shell around the ion. The TIP4P/2005 water model predicts that anions induce faster formation of water clusters than cations of the same magnitude of charge.     

Semiclassical calculation of nonadiabatic thermal rate constants: application to condensed phase reactions

The nonadiabatic transition state theory proposed recently by Zhao et al. [J. Chem. Phys. 121, 8854 (2004)] is extended to calculate rate constants of complex systems by using the Monte Carlo and umbrella sampling methods. Surface hopping molecular dynamics technique is incorporated to take into account the dynamic recrossing effect. A nontrivial benchmark model of the nonadiabatic reaction in the condensed phase is used for the numerical test. It is found that our semiclassical results agree well with those produced by the rigorous quantum mechanical method. Comparing with available analytical approaches, we find that the simple statistical theory proposed by Straub and Berne [J. Chem. Phys. 87, 6111 (1987)] is applicable for a wide friction region although their formula is obtained using Landau-Zener [Phys. Z. Sowjetunion 2, 46 (1932); Proc. R. Soc. London, Ser. A 137, 696 (1932)] nonadiabatic transition probability along a one-dimensional diffusive coordinate. We also investigate how the nuclear tunneling events affect the dependence of the rate constant on the friction.     

Communication: Thermodynamic scaling of the Debye process in primary alcohols

The molecular dynamics of hydrogen-bonded liquids usually does not satisfy the thermodynamic scaling. However, very recently, two opposite conclusions about validity of thermodynamical scaling in monohydroxy alcohol, 2-ethyl-1-hexanol, were presented by Reiser et al. [J. Chem. Phys. 132, 181101 (2010)] and Fragiadakis et al. [J. Chem. Phys. 132, 144505 (2010)]. In this communication we present new experimental results that can explain this ostensible contradiction.     

Describing the component dynamics in miscible polymer blends: towards a fully predictive model

We have recently proposed [D. Cangialosi et al., J. Chem. Phys. 123, 144908 (2005)] an extension of the Adam-Gibbs [J. Chem. Phys. 43, 139 (1965)] theory, combined with the concept of self-concentration, to describe the temperature dependence of the relaxation time for the component segmental dynamics in miscible polymer blends. Thus, we were able to obtain the dynamics of each component in the blend starting from the knowledge of the dynamic and thermodynamic data of the pure polymers, with a single fitting parameter (alpha) which had to be obtained from the fitting of the experimental data. In the present work we demonstrate that this model is also suitable to describe the polymer segmental dynamics in concentrated polymer solutions. From this result we have developed a new route for determining the value of the alpha parameter associated with any given polymer. Once this value is known for the two components of a possible polymer blend, our model for polymer blends dynamics becomes fully predictive.     

Low-temperature nucleation in a kinetic Ising model under different stochastic dynamics with local energy barriers

Using both analytical and simulational methods, we study low-temperature nucleation rates in kinetic Ising lattice-gas models that evolve under two different Arrhenius dynamics that interpose between the Ising states a transition state representing a local energy barrier. The two dynamics are the transition-state approximation [T. Ala-Nissila, J. Kjoll, and S. C. Ying, Phys. Rev. B 46, 846 (1992)] and the one-step dynamic [H. C. Kang and W. H. Weinberg, J. Chem. Phys. 90, 2824 (1989)]. Even though they both obey detailed balance and are here applied to a situation that does not conserve the order parameter, we find significant differences between the nucleation rates observed with the two dynamics, and between them and the standard Glauber dynamic [R. J. Glauber, J. Math. Phys. 4, 294 (1963)], which does not contain transition states. Our results show that great care must be exercised when devising kinetic Monte Carlo transition rates for specific physical or chemical systems.