Multiple branched adaptive steered molecular dynamics.

Steered molecular dynamics, SMD, [S. Park and K. Schulten, J.

Limit of metastability for liquid and vapor phases of water.

We report the limits of superheating of water and supercooling of vapor from Monte Carlo simulations using microscopic models with configurational enthalpy as the order parameter. The superheating limit is well reproduced. The vapor is predicted to undergo spinodal decomposition at a temperature of Tspvap=46±10 °C (0 °C≪Tspvap≪100 °C) under 1 atm.

Communication: Iteration-free, weighted histogram analysis method in terms of intensive variables.

We present an iteration-free weighted histogram method in terms of intensive variables that directly determines the inverse statistical temperature, β(S) = ∂S/∂E, with S the microcanonical entropy. The method eliminates iterative evaluations of the partition functions intrinsic to the conventional approach and leads to a dramatic acceleration of the posterior analysis of combining statistically independent simulations with no loss in accuracy. The synergistic combination of the method with generalized ensemble weights provides insights into the nature of the underlying phase transitions via signatures in β(S) characteristic of finite size systems.

Generalized replica exchange method.

We present a powerful replica exchange method, particularly suited to first-order phase transitions associated with the backbending in the statistical temperature, by merging an optimally designed generalized ensemble sampling with replica exchanges. The key ingredients of our method are parametrized effective sampling weights, smoothly joining ordered and disordered phases with a succession of unimodal energy distributions by transforming unstable or metastable energy states of canonical ensembles into stable ones. The inverse mapping between the sampling weight and the effective temperature provides a systematic way to design the effective sampling weights and determine a dynamic range of relevant parameters.

Relationship between protein folding thermodynamics and the energy landscape.

The origin of protein folding thermodynamics is examined in terms of the energy landscape, employing an off-lattice protein model with scaled non-native attractions, which is continuously tunable between a Go-like model and a highly frustrated system. Extensive statistical temperature molecular dynamics simulations, combined with inherent structure analysis, reveal the intimate connection between the global geometric properties of the energy landscape and the statistical temperature. The basin depth of the energy landscape is shown to play a key role in the first-order-like characteristics of the statistical temperature, which are easily identified by the squared modulus of the potential energy gradient in the microcanonical ensemble.

Replica exchange statistical temperature Monte Carlo.

The replica exchange statistical temperature Monte Carlo algorithm (RESTMC) is presented, extending the single-replica STMC algorithm [J. Kim, J. E.

POLIR: polarizable, flexible, transferable water potential optimized for IR spectroscopy.

A polarizable, flexible and transferable potential for water, POLIR, is presented. In addition to providing a good description of the usual structural and kinetic properties, POLIR correctly describes the vibrational frequencies, absolute infrared intensities, and HOH angle in clusters, liquid water, and ice, offering the possibility of a comprehensive classical theory of vibrational spectroscopy. The high degree of transferability suggests applications to solvation and to water that is confined, interfacial, and under the extreme conditions encountered in the geological and planetary sciences.

Influence of Go-like interactions on global shapes of energy landscapes in beta-barrel forming model proteins: inherent structure analysis and statistical temperature molecular dynamics simulation.

Recently, the native-centric, coarse-grained "Go-like" protein model has gained a renewed popularity because of its computational simplicity and successful description of some key aspects of folding thermodynamics and kinetics. In the present paper, the properties of Go-like models are investigated in terms of the potential energy landscape (PEL). The non-native attractions of the beta-barrel forming BLN model 46-mer are scaled with a parameter 0 < or = lambda < or = 1, to make a continuous tuning of the PEL from multi-funneled and energetically frustrated at lambda = 1 to a perfect funnel including only topological frustration at lambda = 0.

Structure optimization and folding mechanisms of off-lattice protein models using statistical temperature molecular dynamics simulation: Statistical temperature annealing.

The recently proposed statistical temperature molecular dynamics (STMD) algorithm [Kim, Phys. Rev. Lett.

Statistical temperature molecular dynamics: application to coarse-grained beta-barrel-forming protein models.

Recently the authors proposed a novel sampling algorithm, "statistical temperature molecular dynamics" (STMD) [J. Kim et al., Phys.

Inherent structure analysis of protein folding.

An analysis in terms of the inherent structures (IS, local minima) of the multidimensional potential energy landscape is applied to proteins. Detailed calculations are performed for the 46 bead BLN model, which folds into a four-stranded beta-barrel. Enhanced sampling has allowed determination of 239 199 IS states, believed to encompass nearly all the compact, low-energy states, and of well-averaged thermodynamic quantities at low temperature.

Statistical-temperature Monte Carlo and molecular dynamics algorithms.

A simulation method is presented that achieves a flat energy distribution by updating the statistical temperature instead of the density of states in Wang-Landau sampling. A novel molecular dynamics algorithm (STMD) applicable to complex systems and a Monte Carlo algorithm are developed from this point of view. Accelerated convergence for large energy bins, essential for large systems, is demonstrated in tests on the Ising model, the Lennard-Jones fluid, and bead models of proteins.

Induction model for molecular electrostatics: application to the infrared spectroscopy of CO liquid.

Far-infrared intermolecular and midinfrared vibrational spectra of CO liquid have been calculated by Fourier transforming the quantum-corrected classical dipole correlation. The time dependence of the coordinates is determined from a standard nonpolarizable force field, and the dipole is determined from the coordinates with a "spectroscopic model" proposed herein. The model includes intramolecular induction and atomic charges, polarizabilities, and permanent dipoles.