A new program for molecular dynamics (MD) simulation and energy refinement of biological
macromolecules, OPAL, is introduced. Combined with the supporting program TRAJEC for …

1. Introduction 2582. Set-up of MD simulations 2602.1 Constant-pressure dynamics 2602.2
Grand-canonical dynamics 2612.3 Boundary conditions 2613. Force fields 2623.1 Proteins …

A collection of algorithms is presented to allow for the efficient computation of the dynamics
of large systems of macromolecules and solvent. Application of the Fast Multipole Algorithm …

The rapid and accurate molecular dynamics simulation of biomolecules was made possible
by a special purpose computer, MD-GRAPE (GRAvity PipE for Molecular Dynamics), which …

Biological function of biomolecules is accompanied by a wide range of motional behavior.
Accurate modeling of dynamics by molecular dynamics (MD) computer simulations is …

This communication presents results from molecular dynamics (MD) simulations with
AMBER 4.11 and the Cornell et al? force field of three different, fully solvated, fully charged …

Molecular dynamics is an important technique with applications in many areas including
those of drug design, protein engineering, macromolecular structure determination and …

Biomolecular force fields for use in molecular dynamics (MD) simulations of proteins, DNA,
or membranes are generally parametrized against ab initio quantum‐chemical and …

Publisher Summary This chapter discusses the molecular dynamics (MD) simulation
techniques for determination of molecular structures from nuclear magnetic resonance …

NMR is one of the most used techniques to resolve structure of proteins and peptides in
solution. However, inconsistencies may occur due to the fact that a polypeptide may adopt …