Molecular dynamics is a technique used to study the properties of nuclear-related materials by solving Newton's equations of motion for a group of particles iteratively. The particles interact with each other through potential energy functions, allowing for the prediction of the system's dynamical ev...
Software for Direct Comparison of Membrane Scattering Experiments Data to Molecular Dynamics SimulationsUniform size self-assembled unilamellar vesicles (ULVs) can be produced from mixtures of weakly charged short- and long-chain phospholipids. These lipid mixtures self-assemble into bilayered micelles (so...
In this study, molecular dynamics simulations were performed to investigate the effects on single-stranded polynucleotide encapsulation by chitosan and the underlying interaction mechanism between polynucleotide and different types of chitosan with atomic details. It was found that the functional groups of c...
A Molecular Dynamics Computer Simulation Performance Comparison of Java Versus CJavaMolecular dynamicsComputer simulationThe relative performance of molecular dynamics (MD) computer simulations of fluids written in ANSI C is compared to that achieved by a comparable program written in Java. The performance...
A comparison between parallelization approaches in molecular dynamics simulations on GPUs. J. Comput. Chem. 36, 1-8 (2015).Rovigatti, L.; Sulc, P.; Reguly, I.Z.; Romano, F. A Comparison between Parallelization Approaches in Molecular Dynamics Simulations on GPUs. J. Comput. Chem. 2015, ...
Our complex example material is semicrystalline P3HT, and we were able to use our method, along with experimental INS data, to make a valuable, direct comparison between experimental and simulated low energy dynamics. Such a direct comparison with molecular dynamics simulations is not possible with ...
NMR data are particularly useful, as the many receptor and ligand conformations sampled by molecular dynamics simulations can be used to predict NMR measurements like spin relaxation, permitting direct comparison between experimental and theoretical techniques. Indeed, a number of studies have shown good...
NMR data are particularly useful, as the many receptor and ligand conformations sampled by molecular dynamics simulations can be used to predict NMR measurements like spin relaxation, permitting direct comparison between experimental and theoretical techniques. Indeed, a number of studies have shown good...
fibrillin-1 domains cbEGF12-cbEGF13 (PDB ID: 1LMJ)13and cbEGF22-TB4-cbEGF23 (PDB ID: 1UZJ)24, respectively. cbEGF12-cbEGF13 constituted the primary focus of this study. TB4-cbEGF23 was included for comparison. All structures were visualized using Visualize Molecular Dynamics (VMD) 1.9...
these energy values were calculated using CHARMM forcefield incorporated in the Discovery Studio software upon the successful completion of dynamics simulation using COMPASS forcefield. The contribution of the binding is further analysed to be electrostatic and hydrophobic. There exist about 15 hydrogen bo...