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A method for calculating the free energy difference between two structurally defined conformational states of a chemical system is developed. A path is defined using a previously reported collective variable that interpolates between two or more conformations, and a restraint is introduced in order to keep the system close to the path. The evolution of the system along the path, which typically presents a high free energy barrier, is generated using enhanced sampling schemes. Although the formulation of the method in terms of a path is quite general, an important advance in this work is the demonstration that prior knowledge of the path is, in fact, not needed and that the free energy difference can be obtained using a simplified definition of the path collective variable that only involves the endpoints. We first validate this method on cyclohexane isomerization. The method is then tested for an extensive conformational change in a realistic molecular system by calculating the free energy difference between the α-helix and β-hairpin conformations of deca-alanine in solution. Finally, the method is applied to a biologically relevant system to calculate the free energy difference of an observed and a hypothetical conformation of an antigenic peptide bound to a major histocompatibility complex. [ABSTRACT FROM AUTHOR]

Enhanced sampling techniques that target a set of collective variables and that use molecular dynamics as the driving engine have seen widespread application in the computational molecular sciences as a means to explore the free-energy landscapes of complex systems. The use of molecular dynamics as the fundamental driver of the sampling requires the introduction of a time step whose magnitude is limited by the fastest motions in a system. While standard multiple time-stepping methods allow larger time steps to be employed for the slower and computationally more expensive forces, the maximum achievable increase in time step is limited by resonance phenomena, which inextricably couple fast and slow motions. Recently, we introduced deterministic and stochastic resonance-free multiple time step algorithms for molecular dynamics that solve this resonance problem and allow ten- to twenty-fold gains in the large time step compared to standard multiple time step algorithms [P. Minary et al., Phys. Rev. Lett. 93, 150201 (2004); B. Leimkuhler et al., Mol. Phys. 111, 3579-3594 (2013)]. These methods are based on the imposition of isokinetic constraints that couple the physical system to Nosé-Hoover chains or Nos'e-Hoover Langevin schemes. In this paper, we show how to adapt these methods for collective variable-based enhanced sampling techniques, specifically adiabatic free-energy dynamics/temperature-accelerated molecular dynamics, unified free-energy dynamics, and by extension, metadynamics, thus allowing simulations employing these methods to employ similarly very large time steps. The combination of resonance-free multiple time step integrators with free-energy-based enhanced sampling significantly improves the efficiency of conformational exploration. [ABSTRACT FROM AUTHOR]

The numerical algorithms for the discrete variable representation (DVR) basis sets based ab initio molecular dynamics (AIMD) scheme are provided and the accuracy and stability of the implementation of the DVR/AIMD scheme are tested by performing a simulation of liquid water at ambient conditions. The results show that a DVR/AIMD simulation of liquid water in the complete basis set limit is possible with a relatively small number of grid points as compared to the plane wave (PW) basis sets/AIMD method.

The theoretical study of (LiMe)(sub n) aggregates using Car-Parrinello molecular dynamics was undertaken and with respect to a quantum chemical static treatment, this approach furnishes supplementary information about the structural parameters. Results found that parameter-free ab intio molecular dynamics method is introduced.

The (super 17)O NMR parameters of an amorphous calcium aluminisilicate (CAS) is computed from first-principles. The atomic coordinates of a CAS glass of composition (CaO)0.21(Al2O3)0.12(SiO2)0.67 were obtained by quenching a liquid to room temperature by the means of ab initio molecular-dynamics simulations of the Car-Parrinello type.

Author(s): Mark E. Tuckerman (corresponding author) [1]; Dominik Marx [2]; Michele Parrinello [3, 4] Compared to other ions, protons (H[sup.+] ) and hydroxide ions (OH[sup.-] ) exhibit anomalously high mobilities [...]

A study was conducted to investigate the isothermal-isobaric molecular dynamics methods in system subject to holonomic constraints with the goal of devising equations of motion in which the scaling is performed on atomic positions. The result demonstrates that the Kneller-Mulders equations generate an isothermal-isobaric ensemble distribution only for systems with nonzero total force.

The different methods to calculate the accurate vibrational energy relaxation rates for high-frequency modes from classical molecular dynamics simulations are presented. The features and advantages of Fermi's golden rule, a convenient starting point for calculating the vibrational energy relaxation rate constants, are discussed.

A study was conducted to examine the structural and thermodynamic properties of a water droplet enclosed in a spherical cavity embedded in a hydrophobic material. The results indicate that the structure of water near an impenetrable and purely repulsive surface at standard conditions of temperature and pressure is described as a dry, separated state.

A study was conducted to investigate the thermodynamic and structural properties of a Lennard-Jones liquid at a state very close to the triple point as the radius of a hard sphere solute is varied. The result reveals that the oscillatory profiles arise for small, molecular sized radii, where as for large radii smooth interfaces with a drying layer of low vapor density near the solute are seen.

The numerical calculations of the concentration of interstitials in hard-sphere crystals are presented. In a three-dimensional fcc hard-sphere crystal at the melting pint, the concentration of interstitials is 2.7(4) x 10(super -8).

The various important issues related to the implementation of the nonadiabatic dynamics methods in the situation, where quasi-nonavoided crossings take place and play a crucial role in determining the dynamics, are presented. The important connection between dynamics, local environmental symmetry, and electronic structure in determining nonadiabatic relaxation is discussed.

The method of ab initio molecular dynamics was used to study the structural, dynamical, and electronic properties of ionic defects in liquid ammonia at 260 K created by the addition or removal of a proton. The result reveals that the NH4(super +) exhibits a characteristic cationic solvation pattern, in which it donates four hydrogen bonds to neighboring ammonia molecules, giving it a coordination number of 4.

Investigation of crystalline nitric acid trihydrate properties at 195 K has been carried out by means of Car-Parrinello molecular dynamics calculations. Results demonstrate that a proton requires free energy to reach the center of the oxygen-oxygen pair.

Ab initio path integral simulations, including time-independent equilibrium thermal and quantum fluctuations of nuclei, were used to determine interatomic interactions from an electronic structure. The hydrated proton was found to form a fluxional defect in the hydrogen-bonded network. This becomes delocalized over several hydrogen bonds due to quantum fluctuations. The proton is thus considered part of a low-barrier hydrogen bond where tunnelling is slight and the transition-state theory does not apply.