A modification of the nudged elastic band method for finding minimum energy paths is presented. One of the images is made to climb up along the elastic band to converge rigorously on the highest saddle point. Also, variable spring constants are used to increase the density of images near the top of the energy barrier to get an improved estimate of the reaction coordinate near the saddle point. Applications to CH4 dissociative adsorption on Ir~111! and H2 on Si~100! using plane wave based density functional theory are presented. © 2000 American Institute of Physics. @S0021-9606~00!71246-3#

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A climbing image nudged elastic band method for finding saddle points and minimum energy paths

The authors present a new molecular dynamics algorithm for sampling the canonical distribution. In this approach the velocities of all the particles are rescaled by a properly chosen random factor. The algorithm is formally justified and it is shown that, in spite of its stochastic nature, a quantity can still be defined that remains constant during the evolution. In numerical applications this quantity can be used to measure the accuracy of the sampling. The authors illustrate the properties of this new method on Lennard-Jones and TIP4P water models in the solid and liquid phases. Its performance is excellent and largely independent of the thermostat parameter also with regard to the dynamic properties.

Canonical sampling through velocity rescaling

CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecu- lar simulation program. It has been developed over the last three decades with a primary focus on molecules of bio- logical interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estima- tors, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numer- ous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983.

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CHARMM: the biomolecular simulation program.

An improved way of estimating the local tangent in the nudged elastic band method for finding minimum energy paths is presented. In systems where the force along the minimum energy path is large compared to the restoring force perpendicular to the path and when many images of the system are included in the elastic band, kinks can develop and prevent the band from converging to the minimum energy path. We show how the kinks arise and present an improved way of estimating the local tangent which solves the problem. The task of finding an accurate energy and configuration for the saddle point is also discussed and examples given where a complementary method, the dimer method, is used to efficiently converge to the saddle point. Both methods only require the first derivative of the energy and can, therefore, easily be applied in plane wave based density-functional theory calculations. Examples are given from studies of the exchange diffusion mechanism in a Si crystal, Al addimer formation on the Al(100) surfa...

Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points

An analytical algorithm, called SETTLE, for resetting the positions and velocities to satisfy the holonomic constraints on the rigid water model is presented. This method is still based on the Cartesian coordinate system and can be used in place of SHAKE and RATTLE. We implemented this algorithm in the SPASMS package of molecular mechanics and dynamics. Several series of molecular dynamics simulations were carried out to examine the performance of the new algorithm in comparison with the original RATTLE method. It was found that SETTLE is of higher accuracy and is faster than RATTLE with reasonable tolerances by three to nine times on a scalar machine. Furthermore, the performance improvement ranged from factors of 26 to 98 on a vector machine since the method presented is not iterative. © 1992 by John Wiley & Sons, Inc.

SETTLE: an analytical version of the SHAKE and RATTLE algorithm for rigid water models

We present a molecular dynamics computer simulation method for calculating equilibrium constants for the formation of physical clusters of molecules. The method is based on Hill’s formal theory of physical clusters. In the method, a molecular dynamics calculation is used to calculate the average potential energy of a cluster of molecules as a function of temperature, and the equilibrium constants are calculated from the integral of the energy with respect to reciprocal temperature. The method is illustrated by calculations of the equilibrium constants for the formation of clusters of two to five water molecules that interact with each other by an intermolecular potential devised by Watts. The method is compared with other procedures for calculating the thermodynamic properties of clusters.

A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: Application to small water clusters

: We present a molecular dynamics computer simulation method for calculating equilibrium constants for the formation of physical clusters of molecules. The method is based on Hill's formal theory of physical clusters. In the method, a molecular dynamics calculation is used to calculate the average potential energy of a cluster of molecules as a function of temperature, and the equilibrium constants are calculated from the integral of the energy with respect to reciprocal temperature. The method is illustrated by calculations of the equilibrium constants for the formation of clusters of two to five water molecules that interact with each other by an intermolecular potential devised by Watts. The method is compared with other procedures for calculating the thermodynamic properties of clusters. (Author)

Feedback quantum control of molecular electronic population transfer

The photofragment spectrum of NO2 has been measured in the near ultraviolet at 28 810 cm−1. A molecular beam of NO2 is crossed with brief pulses of polarized laser light and measurements are made on the distributions of speed and direction of the recoiling O and NO fragments produced by photodissociation. The average translational energy of the fragments is about 60% of the available energy. There are at least two prominent peaks in the translational energy distribution. We conclude that the two peaks most likely correspond to nearly equal probability of recoil with the NO fragment in the v=0 and v=1 vibrational states. Such vibrationally excited NO fragments produced by photodissociation in polluted atmospheres could perhaps react with different rates than ground state fragments. The positions and widths of the peaks indicate that there is a significant rotational distribution. Statistical and direct models for photodissociation energy partitioning are briefly explored, and their predictions compared wit...

Triatomic Photofragment Spectra: I. Energy Partitioning in NO2 Photodissociation,

The angular distribution of recoil of O atoms from the photodissociation of NO2 at 28 810 cm−1 is presented and analyzed to obtain information about the lifetime and symmetry of the excited dissociative state. The theoretical effects on photofragment angular distributions of excited state symmetry, lifetime, angular momentum, and angular recoil distribution with respect to internal coordinates are considered. The actual angular distribution measured by photofragment spectroscopy, peaks in the direction of the electric vector of the light, indicating that the predominant upper state is of 2B2 symmetry. Some absorption leading to states of different symmetry cannot be excluded. An upper limit for the lifetime of the excited NO2 molecule before dissociation is ∼ 2 × 10−13 sec, indicating that break‐up is too rapid to be affected by collisions in the atmosphere where NO2 photodissociation is an important step in photochemical air pollution.

Kent R. Wilson

Papers

A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: Application to small water clusters

A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: Application to small water clusters

Feedback quantum control of molecular electronic population transfer

Triatomic Photofragment Spectra: I. Energy Partitioning in NO2 Photodissociation,

Triatomic Photofragment Spectra. II. Angular Distributions from NO2 Photodissociation