Experiences with Asynchronous Parallel Molecular Dynamics Simulations

Influences of Small-Scale Effect and Boundary Conditions on the Free Vibration of Nano-Plates: A Molecular Dynamics Simulation

This paper addresses the influence of boundary conditions and small-scale effect on the free vibration of nano-plates using molecular dynamics (MD) and nonlocal elasticity theory. Based on the MD simulations, Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is used to obtain fundamental frequencies of single layered graphene sheets (SLGSs) which modeled in this paper as the mo...

Long Range Corrections to the Vapor-Liquid Equilibrium and Surface Tension of Methane with NVT Molecular Dynamics Simulations

Energy study at different solvents for potassium Channel Protein by Monte Carlo, Molecular and Langevin Dynamics Simulations

Potassium Channels allow potassium flux and are essential for the generation of electric current acrossexcitable membranes. Potassium Channels are also the targets of various intracellular controlmechanisms; such that the suboptimal regulation of channel function might be related to pathologicalconditions. Realistic studies of ion current in biologic channels present a major challenge for compu...

Gyration Radius and Energy Study at Different Temperatures for Acetylcholine Receptor Protein in Gas Phase by Monte Carlo, Molecular and Langevin Dynamics Simulations

The determination of gyration radius is a strong research for configuration of a Macromolecule. Italso reflects molecular compactness shape. In this work, to characterize the behavior of theprotein, we observe quantities such as the radius of gyration and the average energy. We studiedthe changes of these factors as a function of temperature for Acetylcholine receptor protein in gasphase with n...

Experiences Instrumenting a Distributed Molecular Dynamics Program

As cluster computing becomes increasingly more accessible, the need for tools to simplify the development and use of parallel simulations grows proportionally. One class of tools, steering and visualization middle-ware, promises to assist in code development as well as increase the value of the final simulation produced. In this paper we discuss this middle-ware and our experiences instrumentin...