Sentence examples for molecular dynamics module from inspiring English sources

A molecular dynamics module reads a trajectory file of the results of molecular dynamics calculations and animates the structure.

After the system had attained a temperature of 300 K and density of 1 g/cc, production run was carried out for 30 ns in NPT ensemble using PMEMD (Partile Mesh Ewald Molecular Dynamics) module of AMBER.

This article describes the design of the molecular dynamics simulation module, which is based on a domain decomposition, and provides implementation details on the data and communication structure and how the code deals with the complexity of atom redistribution and load balancing.

These results are in excellent agreement with the sequence of events predicted by molecular dynamics simulations of the 10FNIII module.

As a patch code, the VTREMD module performs classical molecular dynamics (MD) with Monte Carlo (MC) decisions between MD runs.

The overall stability of the PvTRAg33.5 model was checked by a molecular dynamics simulation using the CHARMm [34] module on a fully hydrated model.

We initiated molecular dynamics trajectories using a monomeric PH-TH module from a crystal structure which contained neither IP6 nor IP4.

The PMEMD module of the Amber molecular dynamics package (version 10) [ 37] and the Amber ff03 force field [ 38] were used for the MD simulation of the EcDHNA DHNP complex.

All molecular dynamics simulations were performed using the Sander-classic module in the AMBER6 package [20] with the ff96 force field together with Verlet dynamics.

Multiple molecular dynamics simulations (MMDSs) were performed using the PMEMD module of the AMBER 8.0 program [50] with a revised force field (to be published) that is based on the second-generation AMBER force field (frcmod.ff99SB) [51].ff99SB

A driver module for executing volume temperature replica exchange molecular dynamics (VTREMD) was developed for the LAMMPS package.