In order to apply the molecular dynamics (MD) method to simulate modulated phases in organic materials, a compensating external pressure tensor is proposed to compensate for the deficiencies of the force field applied in the simulation. MD can well reproduce modulated phases that have been measured by diffraction. Mechanisms of incommensurate modulation are revealed from the simulations. Detail...

A coarse-grained simulation model for the nucleosome is developed, using a methodology modified from previous work on the ribosome. Protein residues and DNA nucleotides are represented as beads, interacting through harmonic (for neighboring) or Morse (for nonbonded) potentials. Force-field parameters were estimated by Boltzmann inversion of the corresponding radial distribution functions obtain...

We propose a hybrid model, coupling lattice Boltzmann (LB) and molecular dynamics (MD) models, for the simulation of dense fluids. Time and length scales are decoupled by using an iterative Schwarz domain decomposition algorithm. The MD and LB formulations communicate via the exchange of velocities and velocity gradients at the interface. We validate the present LB-MD model in simulations of tw...

Molecular dynamics (MD) is a computer simulation technique where the time evolution of a set of interacting atoms is approximated by integrating their equations of motion. Our goal is to explain the mathematical background of MD for practitioners and researchers in numerical analysis and computational mechanics. The vast majority of these practitioners and researchers work with continuum mechan...

The structure of molten LaBr3 was investigated by X-ray diffraction and molecular dynamics simulations. It was found that the short range structure of molten LaBr3 is very similar to that of molten LaCl3, except for some structural features such as interionic distances based on the difference of anion sizes. In the MD simulation, the shear viscosity of molten LaBr3 was estimated from the struct...

867-Plat Verifying Self-Consistency of Protein Structure and Dynamics through MD Simulation and WAXS Hao Zhou1, Hugo Guterres2, Carla Mattos2, Lee Makowski3. EECE, Northeastern University, Boston, MA, USA, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA, Bioengineering Department, Northeastern University, Boston, MA, USA. Molecular Dynamics (MD) simulation...

We report a general approach for the simulation of the electron paramagnetic resonance (EPR) spectra of spin labels attached to peptides and proteins directly from replica-exchange molecular dynamics (REMD) trajectories. Conventional MD trajectories are generally inadequate for the prediction of EPR line shapes since the label can become trapped in one or more of a set of rotameric states, thus...