To enable a simulation of the growth of crystalline fibers at a cluster of workstations, I developed a parallel molecular-dynamics (MD) algorithm. The structure of the MD algorithm is described briefly, together with its parallelization. Some specific features of our application will be discussed and an illustration of the program performance will be given.

A molecular-level understanding of the function of a protein requires knowledge of both its structural and dynamic properties. NMR spectroscopy allows the measurement of generalized order parameters that provide an atomistic description of picosecond and nanosecond fluctuations in protein structure. Molecular dynamics (MD) simulation provides a complementary approach to the study of protein dyn...

Multiscale computational approach that combines different methods to study laser ablation phenomenon is presented. The methods include the molecular dynamics (MD) breathing sphere model for simulation of the initial stage of laser ablation, a combined MD finite element method (FEM) approach for simulation of propagation of the laser-induced pressure waves out from the MD computational cell, and...

This paper introduces mdFoam+, which is an MPI parallelised molecular dynamics (MD) solver implemented entirely within the OpenFOAM software framework. It is open-source and released under the same GNU General Public License (GPL) as OpenFOAM. The source code is released as a publicly open software repository that includes detailed documentation and tutorial cases. Since mdFoam+ is designed ent...

Recent advances in molecular dynamics (MD) simulation methods and in available computational resources have allowed for more reliable simulations of biological phenomena. From all-atom MD simulations, we are now able to visualize in detail the interactions between antimicrobial peptides (AMPs) and a variety of membrane mimics. This helps us to understand the molecular mechanisms of antimicrobia...

Conformational flexibility of tuftsin molecule is studied using all-atom based atom-atom potential and systematic search, simulated annealing molecular dynamics (SAMD) and molecular dynamics (MD) techniques. Latter was carried out for 650 pico seconds (ps) using AMBER 4.0 with explicit water in TIP3P model. Number of inter-atomic distances and torsional angles were monitored during SAMD and MD ...

in this paper, the stability characteristics of single-walled carbon nanotubes (swcnts) under the action of axial load are investigated. to this end, a nonlocal flügge shell model is developed to accommodate the small length scale effects. the analytical rayleigh-ritz method with beam functions is applied to the variational statement derived from the flügge-type buckling equations. molecular dy...

This paper presents a molecular mechanics study of nanorobotic structures using molecular dynamics (MD) simulations coupled to virtual reality (VR) techniques. The operator can design and characterize through molecular dynamics simulation the behavior of bionanorobotic components and structures through 3-D visualization. The main novelty of the proposed simulations is based on the mechanical ch...