Advances in computational power have greatly facilitated the successful implementation of large-scale computer simulations of biological assemblies and complex condensed phases. Researchers have developed numerous simulation techniques, but many of these share, at their core, the so-called molecular dynamics (MD) paradigm to simulate such systems. (See the “Molecular Dynamics in a Nutshell” sid...

The development of improved epoxy resins can be greatly facilitated using molecular dynamics (MD) techniques. Because molecular-level failure events can play a significant role in epoxy mechanical behavior, the reactive force field (ReaxFF) is an ideal tool for MD simulations of crosslinked epoxies. The results of this study demonstrate that mechanical stiffness and strength values predicted wi...

We study the preferred conformation of the glycosidic linkage of methyl-alpha-mannopyranoside in the gas phase and in aqueous solution. Results obtained utilizing Car-Parrinello molecular dynamics (CPMD) simulations are compared to those obtained from classical molecular dynamics (MD) simulations. We describe classical simulations performed with various water potential functions to study the im...

Fragment molecular orbital molecular dynamics (FMO-MD) with periodic boundary conditions is performed on liquid water using the analytic energy gradient, the electrostatic potential point charge approximation, and the electrostatic dimer approximation. Compared to previous FMO-MD simulations of water that used an approximate energy gradient, inclusion of the response terms to provide a fully an...

The use of coarse-grained (CG) models can significantly increase the time and length scales accessible to computational molecular dynamics (MD) simulations. To address very large-scale phenomena, however, requires a careful consideration of memory requirements and parallel MD load balancing in order to make efficient use of current supercomputers. In this work, a CG-MD code is introduced which ...

Molecular dynamics (MD) simulations allow the investigation of the structural dynamics of biomolecular systems with unrivaled time and space resolution. However, in order to compensate for the inaccuracies of the utilized empirical force fields, it is becoming common to integrate MD simulations with experimental data obtained from ensemble measurements. We review here the approaches that can be...

Anisotropic network model (ANM) is a coarse-grained normal mode analysis that is widely used for describing the collective motions of proteins around their native structure. In this work, protein dynamics along ANM modes are constructed by linear stochastic time series models extracted from molecular dynamics (MD) simulations, and these models are simulated to mimic the dynamics of a relatively...

We present a joint molecular dynamics (MD)/kinetic Monte Carlo (KMC) study aimed at the atomistic description of charge transport in stacks of liquid-crystalline tetraalkoxy-substituted, metal-free phthalocyanines. The molecular dynamics simulations reproduce the major structural features of the mesophases, in particular, a phase transition around 340 K between the rectangular and hexagonal pha...

Staphylococcus aureus protein A (SpA) is the most popular affinity ligand for immunoglobulin G1 (IgG1). However, the molecular basis for the dissociation dynamics of SpA-IgG1 complex is unclear. Herein, coarse-grained (CG) molecular dynamics (MD) simulations with the Martini force field were used to study the dissociation dynamics of the complex. The CG-MD simulations were first verified by the...