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Advanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models and algorithmic improvements that can ameliorate their cost, underdeveloped interfaces and limited dissemination in computational code bases that are widely used in the computational chemistry community, and software implementations that have not kept pace with modern high-performance computing (HPC) architectures, such as multicore CPUs and modern graphics processing units (GPUs). In this Feature Article we review recent progress made in these areas, including well-defined polarization approximations and new multipole electrostatic formulations, novel methods for solving the mutual polarization equations and increasing the MD time step, combining linear-scaling electronic structure methods with new QM/MM methods that account for mutual polarization between the two regions, and the greatly improved software deployment of these models and methods onto GPU and CPU hardware platforms. We have now approached an era where multipole-based polarizable force fields can be routinely used to obtain computational results comparable to state-of-the-art density functional theory while reaching sampling statistics that are acceptable when compared to that obtained from simpler fixed partial charge force fields.

Higher order factorization schemes are developed for path integral molecular dynamics in order to improve the convergence of estimators for physical observables as a function of the Trotter number. The methods are based on the Takahashi-Imada and Susuki decompositions of the Boltzmann operator. The methods introduced improve the averages of the estimators by using the classical forces needed to carry out the dynamics to construct a posteriori weighting factors for standard path integral molecular dynamics. The new approaches are straightforward to implement in existing path integral codes and carry no significant overhead. The Suzuki higher order factorization was also used to improve the end-to-end distance estimator in open path integral molecular dynamics. The new schemes are tested in various model systems, including an ab initio path integral molecular dynamics calculation on the hydrogen molecule and a quantum water model. The proposed algorithms have potential utility for reducing the cost of path integral molecular dynamics calculations of bulk systems. [ABSTRACT FROM AUTHOR]

The ab initio molecular-dynamics formalism of Car and Parrinello is extended to preserve the locality of the orbitals. The supplementary term in the Lagrangian does not affect the nuclear dynamics, but ensures “on the fly” localization of the electronic orbitals within a periodic supercell in the Γ-point approximation. The relationship between the resulting equations of motion and the formation of a gauge-invariant Lagrangian combined with a gauge-fixing procedure is briefly discussed. The equations of motion can be used to generate a very stable and easy to implement numerical integration algorithm. It is demonstrated that this algorithm can be used to compute the trajectory of the maximally localized orbitals, known as Wannier orbitals, in ab initio molecular dynamics with only a modest increase in the overall computer time. In the present paper, the new method is implemented within the generalized gradient approximation to Kohn–Sham density-functional theory employing plane wave basis sets and atomic pseudopotentials. In the course of the presentation, we briefly discuss how the present approach can be combined with localized basis sets to design fast linear scaling ab initio molecular-dynamics methods. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The reference system propagator algorithm of Tuckerman et al. is applied to a simple model of flexible CO2. The forces are broken up according to three different time scales corresponding to the internal motion, short-range impulsive collisions, and long-range interactions, and three time steps are introduced to integrate the equations of motion. The use of this scheme allows a factor of 8 to 12 to be saved in CPU time over standard integration schemes. [ABSTRACT FROM AUTHOR]

New path integral molecular dynamics (PIMD) and path integral hybrid Monte Carlo (PIHMC) algorithms are developed. It is shown that the use of a simple noncanonical change of variables that naturally divides the quadratic part of the action into long and short wavelength modes and multiple time scale integration techniques results in very efficient algorithms. The PIMD method also employs a constant temperature MD technique that has been shown to give canonical averages even for stiff systems. The new methods are applied to the simple quantum mechanical harmonic oscillator and to electron solvation in fluid helium and xenon. Comparisons are made with PIMC and the more basic PIMD and PIHMC methods. [ABSTRACT FROM AUTHOR]

A frequently encountered problem in molecular dynamics is how to treat the long times that are required to simulate condensed systems consisting of mixtures of light and heavy particles. Standard methods require the choice of time step sufficiently small to guarantee stable solution for the low mass component with the consequence that these simulations require a very large number of central processing unit cycles to treat the relaxation of the heavier component. In this note, we present a new method that allows one to use a time step appropriate for the heavy particles. This method uses a similar idea to numerical analytical propogator algorithm, an algorithm we invented to treat high frequency oscillators interacting with low frequency baths and is based on a choice of a reference system for the light particle motions. The method is applied to the case of a liquid containing 864 Lennard-Jones spheres, 824 of these particles having a mass, M=100 and 40 spheres picked at random have a mass m=1. It is shown that molecular dynamics using the new algorithm runs seven to ten times faster than standard methods and this approach as well as suitable generalizations should be very useful for future simulations of quantum and classical condensed matter systems. [ABSTRACT FROM AUTHOR]

Comments on the scientific paper 'Simple Reversible Molecular Dynamics Algorithms for Nose-Hoover Chain Dynamics,' by S. Jang and J.A. Voth. Criticism on the proposed leap-frog algorithms of Jang and Voth; Failure to consider energy conservation in the Nose-Hoover chain dynamics.

When there are high and low frequency motions in systems with long and short range forces a judicious choice of reference system leads to very large accelerations in molecular dynamic (MD) simulations. Building on our previous work where we have developed reference system methods for systems with high frequency oscillators, disparate masses, or long range forces, we present a double reference system method which leads to acceleration of as much as 20 in systems consisting of 864 molecules with Lennard-Jones (12-6) forces. Much larger savings should be achieved when this method is applied to longer range forces and larger systems. [ABSTRACT FROM AUTHOR]

The difficulties encountered in sampling of systems with rough energy landscapes using present methodology significantly limit the impact of simulation on molecular biology, in particular protein folding and design. Here, we present a major methodological development based on a promising new technique, the reference potential spatial warping algorithm (REPSWA) [Z. Zhu et al., Phys. Rev. Lett., 88 (2002), pp. 100201-100204], and present applications to several realistic systems. REPSWA works by introducing a variable transformation in the classical partition function that reduces the volume of phase space associated with a priori known barrier regions while increasing that associated with attractive basins. In this way, the partition function is preserved so that enhanced sampling is achieved without the need for reweighting phase-space averages. Here, a new class of transformations, designed to overcome the barriers induced by intermolecular/nonbonded interactions, whose locations are not known a priori, is introduced. The new transformations are designed to work in synergy with transformations originally introduced for overcoming intramolecular barriers. The new transformation adapts to the fluctuating local environment and is able to handle barriers that arise "on the fly." Thus, the new method is referred to as dynamic contact REPSWA (DC-REPSWA). In addition, combining hybrid Monte Carlo (HMC) with DC-REPSWA allows more aggressive sampling to take place. The combined DC-REPSWA-HMC method and its variants are shown to substantially enhance conformational sampling in long molecular chains composed of interacting single beads and beads with branches. The latter topologies characterize the united residue and united side chain representation of protein structures. [ABSTRACT FROM AUTHOR]

Abstract: The Liouville operator approach is employed to derive a new measure-preserving geometric integrator for molecular dynamics simulations in the isothermal–isobaric (NPT) ensemble. Recently, we introduced such a scheme for NPT simulations with isotropic cell fluctuations in the absence of holonomic constraints [M.E. Tuckerman et al., J. Phys. A 39 (2006) 5629]. Here, we extend this approach to include both fully flexible cell fluctuations and holonomic constraints via a new and simpler formulation of the ROLL algorithm of Martyna et al. [Martyna et al., Mol. Phys. 87 (1996) 1117]. The new algorithm improves on earlier schemes in that it possesses a simpler mathematical structure and rigorously preserves the phase space metric. The new algorithm is illustrated on two example systems, ice and liquid n-decane. [Copyright &y& Elsevier]