Early Experiences Porting the NAMD and VMD Molecular Simulation and Analysis Software to GPU-Accelerated OpenPOWER Platforms.

All-atom molecular dynamics simulations of biomolecules provide a powerful tool for exploring the structure and dynamics of large protein complexes within realistic cellular environments. Unfortunately, such simulations are extremely demanding in terms of their computational requirements, and they present many challenges in terms of preparation, simulation methodology, and analysis and visualization of results. We describe our early experiences porting the popular molecular dynamics simulation program NAMD and the simulation preparation, analysis, and visualization tool VMD to GPU-accelerated OpenPOWER hardware platforms.

New faster CHARMM molecular dynamics engine.

We introduce a new faster molecular dynamics (MD) engine into the CHARMM software package. The new MD engine is faster both in serial (i.e.

Coarse-Grain Model for Glucose, Cellobiose, and Cellotetraose in Water.

We present a coarse-grain (CG) simulation model for aqueous solutions of β-d-glucose, cellobiose, and cellotetraose, based on atomistic simulation data for each system. In the model, three spherical beads are used to represent glucose, and a single bead is used to represent water. For glucose, the force field is calculated using force matching by minimizing the sum of the square differences between forces calculated from atomistic and CG simulations.

Coarse-grained simulations of rapid assembly kinetics for polystyrene-b-poly(ethylene oxide) copolymers in aqueous solutions.

We present a coarse-grained, implicit solvent model for polystyrene-b-poly(ethylene oxide) in aqueous solution and study its assembly kinetics using Brownian dynamics simulations. The polymer is modeled as a chain of freely jointed beads interacting through effective potentials. Coarse-grained force field parameters are determined by matching experimental thermodynamic quantities including radius of gyration, second virial coefficient, aggregation number, and critical micelle concentration.

Electrostatic screening and charge correlation effects in micellization of ionic surfactants.

We have used atomistic simulations to study the role of electrostatic screening and charge correlation effects in self-assembly processes of ionic surfactants into micelles. Specifically, we employed grand canonical Monte Carlo simulations to investigate the critical micelle concentration (cmc), aggregation number, and micellar shape in the presence of explicit sodium chloride (NaCl). The two systems investigated are cationic dodecyltrimethylammonium chloride (DTAC) and anionic sodium dodecyl sulfate (SDS) surfactants.

Implicit solvent models for micellization of ionic surfactants.

We propose a method for parametrization of implicit solvent models for the simulation of the self-assembly of ionic surfactants into micelles. The parametrization is carried out in two steps. The first step involves atomistic molecular dynamics simulations of headgroups and counterions with explicit solvent to determine structural properties.

Self-assembly route for photonic crystals with a bandgap in the visible region.

Three-dimensional photonic crystals, or periodic materials, that do not allow the propagation of photons in all directions with a wavelength in the visible region have not been experimentally fabricated, despite there being several potential structures and the interesting applications and physics that this would lead to. We show using computer simulations that two structures that would enable a bandgap in the visible region, diamond and pyrochlore, can be self-assembled in one crystal structure from a binary colloidal dispersion. In our approach, these two structures are obtained as the large (Mg) and small (Cu) sphere components of the colloidal analogue of the MgCu(2) Laves phase, whose growth can be selected and directed using appropriate wall patterning.

Gas-liquid phase separation in oppositely charged colloids: stability and interfacial tension.

We study the phase behavior and the interfacial tension of the screened Coulomb (Yukawa) restricted primitive model (YRPM) of oppositely charged hard spheres with diameter sigma using Monte Carlo simulations. We determine the gas-liquid and gas-solid phase transitions using free energy calculations and grand-canonical Monte Carlo simulations for varying inverse Debye screening length kappa. We find that the gas-liquid phase separation is stable for kappasigma View Article and Find Full Text PDF

Global phase diagram for the honeycomb potential.

We calculate the global phase diagram using classical statistical mechanics for an isotropic pair potential that has been previously [Rechtsman et al., Phys. Rev.

Re-entrant melting and freezing in a model system of charged colloids.

We studied the phase behavior of charged and sterically stabilized colloids using confocal microscopy in a low polarity solvent (dielectric constant 5.4). Upon increasing the colloid volume fraction we found a transition from a fluid to a body centered cubic crystal at 0.

Melting line of charged colloids from primitive model simulations.

We develop an efficient simulation method to study suspensions of charged spherical colloids using the primitive model. In this model, the colloids and the co- and counterions are represented by charged hard spheres, whereas the solvent is treated as a dielectric continuum. In order to speed up the simulations, we restrict the positions of the particles to a cubic lattice, which allows precalculation of the Coulombic interactions at the beginning of the simulation.

Phase behavior of dipolar hard and soft spheres.

We study the phase behavior of hard and soft spheres with a fixed dipole moment using Monte Carlo simulations. The spheres interact via a pair potential that is a sum of a hard-core Yukawa (or screened-Coulomb) repulsion and a dipole-dipole interaction. The system can be used to model colloids in an external electric or magnetic field.

Critical point of electrolyte mixtures.

The critical behavior of electrolyte mixtures was studied using grand canonical Monte Carlo simulations. Mixtures consist of large multivalent macroions and small monovalent co- and counterions. The system can be viewed as a binary mixture of macroions (with their counterions) and salt (co- and counterion pair).

Ionic colloidal crystals of oppositely charged particles.

Colloidal suspensions are widely used to study processes such as melting, freezing and glass transitions. This is because they display the same phase behaviour as atoms or molecules, with the nano- to micrometre size of the colloidal particles making it possible to observe them directly in real space. Another attractive feature is that different types of colloidal interactions, such as long-range repulsive, short-range attractive, hard-sphere-like and dipolar, can be realized and give rise to equilibrium phases.

Phase diagram of dipolar hard and soft spheres: manipulation of colloidal crystal structures by an external field.

Phase diagrams of hard and soft spheres with a fixed dipole moment are determined by calculating the Helmholtz free energy using simulations. The pair potential is given by a dipole-dipole interaction plus a hard-core and a repulsive Yukawa potential for soft spheres. Our system models colloids in an external electric or magnetic field, with hard spheres corresponding to uncharged and soft spheres to charged colloids.

Phase diagrams of hard-core repulsive Yukawa particles.

We determine the phase behavior of hard spheres interacting with repulsive Yukawa (screened Coulomb) interaction using computer simulations. We study the effect of the hard-core diameter on the phase behavior of repulsive Yukawa particles by comparing our phase diagrams with that of repulsive point Yukawa particles. We show that for sufficiently high contact values of the pair potential (betaepsilon=20, 39, 81, and higher), the fluid-face-centered-cubic (fcc) solid, at high screening, the fluid-body-centered-cubic (bcc) solid and the bcc-fcc coexistence for packing fractions eta less, similar 0.