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 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 dynamic "evolution" of the ...

simulation A simulation is the imitation of the operation of a real-world process or system over time. Simulations require the use of Conceptual model, models; the model represents the key characteristics or behaviors of the selected system or proc ...

, and a related computer

software Software is a set of computer programs and associated documentation and data. This is in contrast to hardware, from which the system is built and which actually performs the work. At the lowest programming level, executable code consists ...

package. Both are developed at the

University of Groningen The University of Groningen (abbreviated as UG; nl, Rijksuniversiteit Groningen, 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 in ...

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

ETH Zurich (colloquially) , former_name = eidgenössische polytechnische Schule , image = ETHZ.JPG , image_size = , established = , type = Public , budget = CHF 1.896 billion (2021) , rector = Günther Dissertori , president = Joël Mesot , ac ...

). At Groningen,

Herman Berendsen Herman Johan Christiaan Berendsen (22 September 1934 – 7 October 2019) was a Dutch chemist. He was a professor of physical chemistry at the University of Groningen from 1967 to 1999. Career Berendsen was born on 22 September 1934 in Apeldoorn. I ...

was involved in its development. 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 which ...

Versions

GROMOS87

Aliphatic and aromatic

hydrogen Hydrogen is the chemical element with the symbol H and atomic number 1. Hydrogen is the lightest element. At standard conditions hydrogen is a gas of diatomic molecules having the formula . It is colorless, odorless, tasteless, non-toxic, an ...

atoms were included implicitly by representing the

carbon Carbon () is a chemical element with the symbol C and atomic number 6. It is nonmetallic and tetravalent In chemistry, the valence (US spelling) or valency (British spelling) of an element is the measure of its combining capacity with o ...

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, the 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 electronic bond; they are comparatively weak and th ...

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 hydrophobic, and their odors are usually weak or ex ...

s, and on

amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha am ...

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."The GROMOS software for biomolecular simulation: GROMOS05". Christen M, Hünenberger PH, Bakowies D, Baron R, Bürgi R, Geerke DP, Heinz TN, Kastenholz MA, Kräutler V, Oostenbrink C, Peter C, Trzesniak D, van Gunsteren WF. ''J Comput Chem 26'' (16): 1719–51

GROMOS11

The current GROMOS release is dated in May 2011.

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 residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...

nucleotide Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules wi ...

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, fructose, and galactose. Compound sugars, also called disaccharides or double ...

s. The B-version applies to isolated

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

s (gas phase).

54

* 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 naturally-occurring molecules which includes fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids, and others. The functions of lipids include ...

aggregates such as membranes and

micelle A micelle () or micella () (plural micelles 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 collo ...

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

polymer A polymer (; Greek '' poly-'', "many" + ''-mer'', "part") is a substance or material consisting of very large molecules called macromolecules, composed of many repeating subunits. Due to their broad spectrum of properties, both synthetic a ...

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 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