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of the hour:
Daniel Hießl
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Biomolecular dynamics simulations of
proteins, DNA, ligands.
HOOMD-blue stands for Highly Optimized Object-oriented Many-particle Dynamics -- Blue Edition
Software Tools for Molecular Design.
DL_POLY is a general purpose serial and parallel molecular dynamics simulation package.
Zodiac is a molecular modelling suite for computation, analysis and display of molecular data.
Ghemical is computational chemistry package.
AmberFFC creates the AMBER & GLYCAM FF for the Accelrys molecular mechanics modules.
GULP is a program for performing a variety of types of simulation on materials using boundary conditions of 0-D (molecules and clusters), 1-D (polymers), 2-D (surfaces, slabs and grain boundaries), or 3-D (periodic solids).
Towhee is a Monte Carlo molecular simulation code originally designed for the prediction of fluid phase equilibria using atom-based force fields and the Gibbs ensemble with particular attention paid to algorithms addressing molecule conformation sampling.
MMC is a Metropolis Monte Carlo program for the simulation of molecular assemblies in the canonical, grand-canonical and isothermal-isobaric ensembles.
Simulaid will help you for the description of the interaction energy terms, of the molecules in the system and of the boundary conditions.
AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
Hippo is a software package for simulation and analysis of bio-molecules at an atomic level. It has been specifically developed for very efficient protein folding studies in aqueous and membrane environments.
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