GROMOS

GROMOS is a force field for molecular dynamics simulation developed at the University of Groningen and the ETH Zurich. GROMOS is also the name for the molecular dynamics simulation package associated with this force field.

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GROMOS^TM is a general-purpose molecular dynamics computer simulation package for the study of biomolecular systems. Its purpose is threefold:

- simulation of arbitrary molecules in solution or crystalline state by the method of molecular dynamics (MD), stochastic dynamics (SD) or the path-integral method.

- energy minimisation of arbitrary molecules.

- analysis of conformations obtained by experiment or by computer simulation.

The simulation package comes with the GROMOS force field (proteins, nucleotides, sugars, etc.) the quality of which should be judged from the scientific literature concerning its application to chemical and physical systems, ranging from glasses and liquid crystals to polymers and crystals and solutions of biomolecules.

Interesting applications of GROMOS96 (the latest version of GROMOS) are:

- prediction of the dependence of a molecular conformation on the type of environment (water, methanol, chloroform, DMSO, apolar solvent, crystal, etc.);

- calculation of relative binding constants by evaluating free energy differences between various molecular complexes using thermodynamic integration, perturbation and extrapolation;

- prediction of energetic and structural changes caused by modification of amino acids in enzymes or of base pairs in DNA;

- derivation of three-dimensional (3D) molecular structure on the basis of NMR data by using restrained MD techniques including time-averaged distance- and J-value restraining;

- dynamic modelling of molecular complexes by searching configuration space using MD or SD in 3- or 4-dimensions, soft-core interaction, local elevation search;

- prediction of properties of materials under extreme conditions of temperature and pressure, which may be experimentally inaccessible.

The force field was optimized with respect to the condensed phase properties of alkanes.

See also

• Gromacs
• MOSCITO