Bioinformatics Molecular Dynamics

GROMOS

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GROMOS stands for GROningen MOlecular Simulation computer program package, which has been developed since 1978 for the dynamic modelling of (bio) molecules, until 1990 at the University of Groningen, The Netherlands, and since then at the ETH, the Swiss Federal Institute of Technology, in Zürich, Switzerland. Its development was driven by the research group of Wilfred van Gunsteren. 

Since the last official release of the GROMOS software and manual in 1996, called GROMOS96, no comprehensive release occurred till 2011. The programming language has been changed from FORTRAN to C++, the documentation has been put into electronic form, and many new features have been included in this software.

GROningen MOlecular Simulation (GROMOS) is the name of a force field for molecular dynamics simulation, and a related computer software package. It also incorporates its own force field covering proteins, nucleotides, sugars etc. and can be used to chemical and physical systems ranging from glasses and liquid crystals, to polymers and crystals and solutions of biomolecules.

GROMACS supports the GROMOS force fields, with all parameters provided in the distribution for 43a1, 43a2, 43b1, 45a3, 53a5 and 53a6. The GROMOS force fields are united atom force fields that are without explicit aliphatic (non-polar) hydrogens.

Biomolecular simulation involves four major challenges;

  • the force field must faithfully represent the atomic and molecular interactions
  • the conformational space must be sampled in a manner which is both fast and efficient
  • a Boltzmann configurational ensemble must be generated in order to reproduce thermodynamic quantities 
  • appropriate experimental data must be available against which the simulations can be validated

Versions of GROMOS

GROMOS87

Aliphatic and aromatic hydrogen atoms were included implicitly by representing the carbon atom and attached hydrogen atoms as one group centered on the carbon atom, a united atom force field. The van der Waals force parameters were derived from calculations of the crystal structures of hydrocarbons, and on amino acids using short (0.8 nm) non-bonded cutoff radii. 

GROMOS96

In 1996, a substantial rewrite of the software package was released. The force field was also improved, such as in the following way: aliphatic CHn groups were represented as united atoms with van der Waals interactions re-parameterized on the basis of a series of molecular dynamics simulations of model liquid alkanes using long (1.4 nm) non-bonded cutoff radii. This version is continually being refined and several different parameter sets are available. GROMOS96 includes studies of molecular dynamics, stochastic dynamics, and energy minimization. The energy component was also part of the prior GROMOS, named GROMOS87. GROMOS96 was planned and conceived during a time of 20 months. The package is made of 40 different programs, each with a different essential function. 

GROMOS05

An updated version of the software package was introduced in 2005. 

GROMOS11

It was released in 2011.

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