GROningen MOlecular Simulation (GROMOS) is the name of a force field for

molecular dynamics Molecular dynamics (MD) is a computer simulation method for analyzing the Motion (physics), physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamics ( ...

simulation A simulation is an imitative representation of a process or system that could exist in the real world. In this broad sense, simulation can often be used interchangeably with model. Sometimes a clear distinction between the two terms is made, in ...

, and a related computer

software Software consists of computer programs that instruct the Execution (computing), execution of a computer. Software also includes design documents and specifications. The history of software is closely tied to the development of digital comput ...

package, which has been developed until 1990 at the

University of Groningen The University of Groningen (abbreviated as UG; , abbreviated as RUG) is a Public university#Continental Europe, public research university of more than 30,000 students in the city of Groningen (city), Groningen, Netherlands. Founded in 1614, th ...

, and at the Computer-Aided Chemistry Group at the Laboratory for Physical Chemistry at the Swiss Federal Institute of Technology (

ETH Zurich ETH Zurich (; ) is a public university in Zurich, Switzerland. Founded in 1854 with the stated mission to educate engineers and scientists, the university focuses primarily on science, technology, engineering, and mathematics. ETH Zurich ran ...

). At Groningen, Herman Berendsen was involved in its development. The development is currently a collaborative effort between the research group of Wilfred van Gunsteren, the research groups of Philippe Hünenberger and Sereina Riniker at ETH Zurich, Chris Oostenbrink at the University of Natural Resources and Life Sciences in Vienna, Austria, and Niels Hansen at the University of Stuttgart in Stuttgart, Germany. The united atom force field was optimized with respect to the condensed phase properties of

alkane In organic chemistry, an alkane, or paraffin (a historical trivial name that also has other meanings), is an acyclic saturated hydrocarbon. In other words, an alkane consists of hydrogen and carbon atoms arranged in a tree structure in whi ...

Versions

GROMOS87

Aliphatic and aromatic

hydrogen Hydrogen is a chemical element; it has chemical symbol, symbol H and atomic number 1. It is the lightest and abundance of the chemical elements, most abundant chemical element in the universe, constituting about 75% of all baryon, normal matter ...

atoms were included implicitly by representing the

carbon Carbon () is a chemical element; it has chemical symbol, symbol C and atomic number 6. It is nonmetallic and tetravalence, tetravalent—meaning that its atoms are able to form up to four covalent bonds due to its valence shell exhibiting 4 ...

atom and attached hydrogen atoms as one group centered on the carbon atom, a united atom force field. The

van der Waals force In molecular physics and chemistry, the van der Waals force (sometimes van der Waals' force) is a distance-dependent interaction between atoms or molecules. Unlike ionic or covalent bonds, these attractions do not result from a chemical elec ...

parameters were derived from calculations of the crystal structures of

hydrocarbon In organic chemistry, a hydrocarbon is an organic compound consisting entirely of hydrogen and carbon. Hydrocarbons are examples of group 14 hydrides. Hydrocarbons are generally colourless and Hydrophobe, hydrophobic; their odor is usually fain ...

s, and on

amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although over 500 amino acids exist in nature, by far the most important are the 22 α-amino acids incorporated into proteins. Only these 22 a ...

s using short (0.8 nm) nonbonded cutoff radii.

GROMOS96

In 1996, a substantial rewrite of the software package was released. The force field was also improved, e.g., in the following way: aliphatic CH_n groups were represented as united atoms with van der Waals interactions reparametrized on the basis of a series of molecular dynamics simulations of model liquid

s using long (1.4 nm) nonbonded 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. An example of two important programs within the GROMOS96 are PROGMT, in charge of constructing molecular topology and also PROPMT, changing the classical molecular topology into the path-integral molecular topology.

GROMOS05

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

GROMOS11 version 1.6.1

The current GROMOS version was released in November 2023 and updated in April 2024. New functionalities such as support fir virtual atoms with non-bonded interactions, shifted reaction-field, buffer region neural network, combined TI with (A-)EDS and selective Gaussian accelerated MD.

Parameter sets

Some of the force field parameter sets that are based on the GROMOS force field. The A-version applies to aqueous or

apolar In chemistry, polarity is a separation of electric charge leading to a molecule or its chemical groups having an electric dipole moment, with a negatively charged end and a positively charged end. Polar molecules must contain one or more polar ...

solutions of

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...

nucleotide Nucleotides are Organic compound, organic molecules composed of a nitrogenous base, a pentose sugar and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both o ...

s, and

sugar Sugar is the generic name for sweet-tasting, soluble carbohydrates, many of which are used in food. Simple sugars, also called monosaccharides, include glucose Glucose is a sugar with the Chemical formula#Molecular formula, molecul ...

s. The B-version applies to isolated

molecule A molecule is a group of two or more atoms that are held together by Force, attractive forces known as chemical bonds; depending on context, the term may or may not include ions that satisfy this criterion. In quantum physics, organic chemi ...

s (gas phase).

54

* 54A8 - recalibration of the nonbonded interaction parameters for the charged amino-acid side chains, based on ionic side chain analogs. * 54A7Schmid N., Eichenberger A., Choutko A., Riniker S., Winger M., Mark A. & van Gunsteren W., "Definition and testing of the GROMOS force-field versions 54A7 and 54B7", ''European Biophysics Journal'', 40(7), (2011), 843–85

- 53A6 taken and adjusted torsional angle terms to better reproduce helical propensities, altered N–H, C=O repulsion, new CH₃ charge group, parameterisation of Na⁺ and Cl⁻ to improve free energy of hydration and new improper dihedrals. * 54B7 - 53B6 ''in vacuo'' taken and changed in same manner as 53A6 to 54A7.

53

* 53A5Oostenbrink C., Villa, A., Mark, A. E., and van Gunsteren, W., "A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6", ''Journal of Computational Chemistry'', 25, (2004), 1656–167

- optimised by first fitting to reproduce the thermodynamic properties of pure liquids of a range of small polar molecules and the solvation free enthalpies of amino acid analogs in cyclohexane, is an expansion and renumbering of 45A3. * 53A6 - 53A5 taken and adjusted partial charges to reproduce hydration free enthalpies in water, recommended for simulations of biomolecules in explicit water.

45

* 45A3Schuler, L. D., Daura, X., and van Gusteren, W. F., An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase, ''Journal of Computational Chemistry'' 22(11), (2001), 1205–121

- suitable to apply to

lipid Lipids are a broad group of organic compounds which include fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids, and others. The functions of lipids include storing ...

aggregates such as

membrane A membrane is a selective barrier; it allows some things to pass through but stops others. Such things may be molecules, ions, or other small particles. Membranes can be generally classified into synthetic membranes and biological membranes. Bi ...

s and

micelle A micelle () or micella () ( or micellae, respectively) is an aggregate (or supramolecular assembly) of surfactant amphipathic lipid molecules dispersed in a liquid, forming a colloidal suspension (also known as associated colloidal system). ...

s, for mixed systems of aliphatics with or without water, for

polymer A polymer () is a chemical substance, substance or material that consists of very large molecules, or macromolecules, that are constituted by many repeat unit, repeating subunits derived from one or more species of monomers. Due to their br ...

s, and other apolar systems that may interact with different biomolecules. * 45A4Soares, T. A., Hünenberger, P. H., Kastenholz, M. A., Kräutler, V., Lenz, T., Lins, R. D., Oostenbrink, C., and van Gunsteren, W. F., An improved nucleic acid parameter set for the GROMOS force field, ''Journal of Computational Chemistry'', 26(7), (2005), 725–737

- 45A3 reparameterised to improve

DNA Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...

representation.

43

* 43A1van Gunsteren, W. F., Billeter, S. R., Eking, A. A., Hiinenberger, P. H., Kriiger, P., Mark, A. E., Scott, W. R. P. and Tironi, I. G., ''Biomolecular Simulation, The GROMOS96 Manual and User Guide'', vdf Hochschulverlag AG an der ETH Ziirich and BIOMOS b.v., Zurich, Groningen, 1996. * 43A2

References

External links

* {{DEFAULTSORT:Gromos C++ software Fortran software Molecular dynamics software Force fields (chemistry)