Thermodynamics of Oleic Acid Aggregation from Coarse-Grained Molecular Dynamics Simulations

Coarse-grained molecular dynamics simulations of biomolecules

Coarse-grained molecular dynamics (CGMD) simulations are increasingly being used to analyze the behaviors of biological systems. When appropriately used, CGMD can simulate the behaviors of molecular systems several hundred times faster than elaborate all-atom molecular dynamics simulations with similar accuracy. CGMD parameters for lipids, proteins, nucleic acids, and some artificial substances...

Coarse-grained protein molecular dynamics simulations.

A limiting factor in biological science is the time-scale gap between experimental and computational trajectories. At this point, all-atom explicit solvent molecular dynamics (MD) are clearly too expensive to explore long-range protein motions and extract accurate thermodynamics of proteins in isolated or multimeric forms. To reach the appropriate time scale, we must then resort to coarse grain...

Molecular Dynamics Simulations of Freezing Behavior of Pure Water and 14% Water-NaCl Mixture Using the Coarse-Grained Model

 We performed molecular dynamics simulations using the coarse-grained model to study the freezing behavior of pure water and 14% water-salt mixture in a wide range of temperatures for a very long time around 50 nanoseconds. For the salty water, an interface in nanoscale was used. For both systems, the f...

Coarse Grained Molecular Dynamics

Coarse Grained Molecular Dynamics Simulations of Transmembrane Protein-Lipid Systems

Many biological cellular processes occur at the micro- or millisecond time scale. With traditional all-atom molecular modeling techniques it is difficult to investigate the dynamics of long time scales or large systems, such as protein aggregation or activation. Coarse graining (CG) can be used to reduce the number of degrees of freedom in such a system, and reduce the computational complexity....