GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics simulation package originally developed in the University of Groningen.
It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.
AtomEye is atomistic visualization software fast enough to handle output of molecular dynamics simulations with millions of atoms. It includes parallel and perspective projections with full three-dimensional navigation, customizable bond and coordination number calculation, colour-encoding of arbitrary user-defined quantities, local atomic strain invariant, coloured atom tiling and tracing, up to......
DL_POLY is general purpose serial and parallel molecular dynamics simulation software developed at Daresbury Laboratory by W. Smith, T.R. Forester and I.T. Todorov.DL_POLY_4 is supplied to individuals under an academic licence, which is free of cost to academic scientists pursuing scientific research of a non-commercial nature.......
LAMMPS ("Large-scale Atomic/Molecular Massively Parallel Simulator") is a molecular dynamics program from Sandia National Laboratories.LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic,......
Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems.The JmolApplet is a web browser applet that can be integrated into web pages.The Jmol application is a standalone Java application that......
BioBlender is a software package built on the open-source 3D modeling software Blender .Biology works at nanoscale, with objects invisible to the human eye. With BioBlender it is possible to show some of the characters that populate our cells, based on scientific data and the highest standard of 3D......
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