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 demon...

Protein structure and function are highly dependent on the environmental pH. However, the temporal or spatial resolution of experimental approaches hampers direct observation of pH-induced conformational changes at the atomic level. Molecular dynamics (MD) simulation strategies (e.g. constant pH MD) have been developed to bridge this gap. However, one frequent problem is the sampling of unreali...

We investigate the probability distribution functions of the free flight time and of the number of collisions in a hard-sphere gas at equilibrium. At variance with naive expectation, the latter quantity does not follow Poissonian statistics, even in the dilute limit, which is the focus of the present analysis. The corresponding deviations are addressed both numerically and analytically. In writ...

The distortion of structure of a simple, inverse-12, soft-disk fluid undergoing two-dimensional plane Couette flow was studied by nonequilibrium molecular dynamics (NEMD) simulation and by equilibrium Monte Carlo (MC) simulation with a nonequilibrium potential, under which the equilibrium structure of the fluid is that of the nonequilibrium fluid. Extension of the iterative predictor-corrector ...

Presented in the context of classical molecular mechanics and dynamics are multilevel summation methods for the fast calculation of energies/forces for pairwise interactions, which are based on the hierarchical interpolation of interaction potentials on multiple grids. The concepts and details underlying multigrid interpolation are described. For integration of molecular dynamics the use of dif...

CAMRAD II is an aeromechanical analysis of helicopters and rotorcraft that incorporates a combination of advanced technology, including multibody dynamics, nonlinear finite elements, and rotorcraft aerodynamics. For the design, testing, and evaluation of rotors and rotorcraft; at all stages, including research, conceptual design, detailed design, and development; it calculates performance, load...

In constant pH molecular dynamics simulations, the protonation states of titratable sites can respond to changes of the pH and of their electrostatic environment. Consequently, the number of protons bound to the biomolecule, and therefore the overall charge of the system, fluctuates during the simulation. To avoid artifacts associated with a non-neutral simulation system, we introduce an approa...