Classical molecular dynamics (MD) simulations are employed as a tool to investigate structural properties of ice crystals under several temperature and pressure conditions. All ice crystal phases are analyzed by means of a computational protocol based on a clustering approach following standard MD simulations. The MD simulations are performed by using a recently published classical interaction ...

Virtual laboratory MolDynGrid has been established for computational researches in structural biology and bioinformatics, especially for molecular dynamics (MD) simulations of biological macromolecules and their complexes. Biomolecular simulation usually requires a very high processing power and huge storage space for MD trajectories. In this study we describe the development of virtual laborat...

Molecular Dynamics (MD) and Monte Carlo (MC) simulations are the most popular simulation techniques for many-particle systems. Although they are often applied to similar systems, it is unclear to which extent one has to expect quantitative agreement of the two simulation techniques. In this work, we present a quantitative comparison of MD and MC simulations in the microcanonical ensemble. For t...

We present a simple method for calculating a continuum temperature field directly from a molecular dynamics (MD) simulation. Using the idea of a projection matrix previously developed for use in the bridging scale, we derive a continuum temperature equation which only requires information that is readily available from MD simulations, namely the MD velocity, atomic masses and Boltzmann constant...

We describe the derivation of a set of bonded and nonbonded coarse-grained (CG) potential functions for use in implicit-solvent Brownian dynamics (BD) simulations of proteins derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acids. Bonded potential functions were derived from 1 μs MD simulations of each of the 20 canonical amino acids, with histidine modeled in...

Numerical algorithms are developed for the centroid molecular dynamics (centroid MD) method to calculate dynamical time correlation functions for general many-body quantum systems. Approaches based on the normal mode path integral molecular dynamics and staging path integral Monte Carlo methods are described to carry out a direct calculation of the force on the centroid variables in the centroi...

Neutron diffraction with isotopic substitution (NDIS) experiments and molecular dynamics (MD) simulations have been used to characterize the structure of aqueous guanidinium carbonate (Gdm2CO3) solutions. The MD simulations found very strong hetero-ion pairing in Gdm2CO3 solution and were used to determine the best structural experiment to demonstrate this ion pairing. The NDIS experiments conf...

based on the notion of micro-structure in linear elasticity presented by mindlin, a newextended continuum mechanics (ecm) formulation is derived which can be utilized to model thematerial behavior at atomic scale. an attempt has been made to present a formulation capable ofproducing the molecular dynamics (md) simulation results with less computational effort. to thisend, some new kinematical v...

Molecular dynamics (MD) simulations are useful tools for structure-based drug design. We review recent publications in which explicit solvent MD was used at the initial or final stages of high-throughput docking campaigns. In some cases, MD simulations of the protein target have been carried out before docking to generate a conformer of the protein which differs from the available crystal struc...