Sentence examples for molecular dynamics packages from inspiring English sources

Several popular molecular dynamics packages have already been ported for MDGRAPE-2, including Amber-6 and CHARMM.

METAGUI is based on the output format of the PLUMED plugin, making it compatible with a number of different molecular dynamics packages like AMBER, NAMD, GROMACS and several others.

It is worthy to note that some molecular dynamics packages commonly employed for energy refinement, with particular concern to AMBER [ 40], can be also performed using GPGPU architectures.

A parallel implementation of coupled spin lattice dynamics in the LAMMPS molecular dynamics package is presented.

To ensure fair comparison, all the potentials are used as implemented in the molecular dynamics package LAMMPS.

A general purpose, scalable parallel molecular dynamics package for simulations of arbitrary mixtures of flexible or rigid molecules is presented.

A new wall potential model is developed by using the electronegativity-equalization method (EEM), a ReaxFF empirical force field and a non-reactive molecular dynamics package PumMa.

We present a software module which allows one to efficiently perform molecular dynamics and local minimization calculations in internal coordinates when incorporated into a molecular dynamics package.

We review software development efforts in the LAMMPS molecular dynamics package that have been implemented in order to utilize hybrid high performance computers.

Recently, we have implemented a new QM/MM method (Fireball/Amber), which combines an efficient density functional theory method (Fireball) and a well-recognized molecular dynamics package (Amber), offering an excellent balance between accuracy and sampling capabilities.

Recently, the 3D-RISM-KH theory was coupled with MD simulations by contracting solvent degrees of freedom to treat solvated biomolecules, and the MD/3D-RISM-KH multiscale method was implemented in the Amber molecular dynamics package [T. Luchko et al., 2010, [29]].