Automated Topology Builder (ATB)

The Automated Topology Builder (ATB) is an online repository for molecular topologies, structures and pre-equilibrated systems for GROMOS, GROMACS and CNS. Any visitor to the site can submit a small molecule to the builder to build a new topology. Also, manually curated topologies of specific molecules may be downloaded.

The primary simulation software packages to which the group contributes are GROMOS and GROMACS. Most of this software is available in the public domain, or are available at a nominal cost to academic users.

GROMOS (GROningen MOlecular Simulation library)

GROMOS is a general-purpose molecular dynamics computer simulation package for the study of biomolecular systems, developed within the group of Professor Wilfred van Gunsteren (ETH), Zurich. See: Its primary aim is threefold:

GROMACS (GROningen MAchine for Chemical Simulation)

The GROMACS software package runs on various computer types and is free for non-comercial use. Features of the software include:

  1. Standard Molecular Dynamics simulation
  2. Energy minimisation
  3. NMR Refinement using NOE data
  4. Flexible force field usage
  5. Non-Equilibrium Molecular Dynamics
  6. Various analysis tools

For more information, please see the GROMACS home page.

This page was last updated on July the 10th, 2017.

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