GROMOS

GROningen MOlecular Simulation (GROMOS) is the name of a force field for molecular dynamics simulation, and a related computer software package, which has been developed until 1990 at the University of Groningen, and at the Computer-Aided Chemistry Group<ref>Computer-Aided Chemistry Group, ETH Zurich</ref> at the Laboratory for Physical Chemistry<ref>Laboratory for Physical Chemistry, ETH Zurich</ref> at the Swiss Federal Institute of Technology (ETH Zurich). At Groningen, Herman Berendsen was involved in its development.<ref>Template:Cite web</ref> 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 BOKU University 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 alkanes,<ref name="Shuler2001">Template:Cite journal</ref> polar molecules <ref name="Oostenbrink2004">Template:Cite journal</ref> and charged molecules.<ref>Template:Cite journal</ref>

Versions

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) nonbonded cutoff radii.<ref>W. F. van Gunsteren and H. J. C. Berendsen, Groningen Molecular Simulation (GROMOS) Library Manual, BIOMOS b.v., Groningen, 1987.</ref>

GROMOS96

In 1996, a substantial rewrite of the software package was released.<ref>van Gunsteren, W. F.; Billeter, S. R.; Eising, A. A.; Hünenberger, P. H.; Krüger, P.; Mark, A. E.; Scott, W. R. P.; Tironi, I. G. Biomolecular Simulation: The GROMOS96 Manual and User Guide; vdf Hochschulverlag AG an der ETH Zürich and BIOMOS b.v.: Zürich, Groningen, 1996.</ref><ref>"The GROMOS Biomolecular Simulation Program Package", W. R. P. Scott, P. H. Huenenberger, I. G. Tironi, A. E. Mark, S. R. Billeter, J. Fennen, A. E. Torda, T. Huber, P. Krueger and W. F. van Gunsteren. J. Phys. Chem. A, 103, 3596–3607.</ref> 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 alkanes using long (1.4 nm) nonbonded cutoff radii.<ref>"An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase". Journal of Computational Chemistry 22 (11), August 2001, 1205–1218 by Lukas D. Schuler, Xavier Daura, Wilfred F. van Gunsteren.</ref> 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.<ref>Template:Cite journal</ref>

GROMOS11 version 1.6.1

The current GROMOS version was released in November 2023 and updated in April 2024. Since the release of GROMOS11, the package consists of two subpackages: gromos++ and md++. The gromos++ package consists of a large number of smaller programs, which can be helpful to setup and analyse molecular simulations. The md++ package contains the actual MD engines, which can perform energy minimisations, stochastic dynamic simulations and molecular dynamics simulations. These can incorporate (alchemical) free energy calculations or enhanced sampling methods.

New functionalities of the 1.6.1 release include support for virtual atoms with non-bonded interactions, shifted reaction-field,<ref>Template:Cite journal</ref> buffer region neural network,<ref>Template:Cite journal</ref> combined TI with (A-)EDS<ref>Template:Cite journal</ref> and selective Gaussian accelerated MD.<ref>Template:Cite journal</ref>

Parameter sets

Some of the force field parameter sets that are based on the GROMOS force field. The A-version applies to condensed phase solutions of proteins, nucleotides, and sugars. The B-version applies to isolated molecules (gas phase).

54

• 54A8<ref>Template:Cite journal</ref> - recalibration of the nonbonded interaction parameters for the charged amino-acid side chains, based on ionic side chain analogs.
• 54A7<ref name="Schmid2011">Template:Cite journal</ref> - 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<ref name="Schmid2011"/> - 53B6 in vacuo taken and changed in same manner as 53A6 to 54A7.

53

• 53A5<ref name="Oostenbrink2004">Template:Cite journal</ref> - 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<ref name="Oostenbrink2004"/> - 53A5 taken and adjusted partial charges to reproduce hydration free enthalpies in water, recommended for simulations of biomolecules in explicit water.

45

• 45A3<ref name="Shuler2001">Template:Cite journal</ref> - suitable to apply to lipid aggregates such as membranes and micelles, for mixed systems of aliphatics with or without water, for polymers, and other apolar systems that may interact with different biomolecules.
• 45A4<ref name="Soares2005">Template:Cite journal</ref> - 45A3 reparameterised to improve DNA representation.

43

• 43A1<ref name="G96Manual">van 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.</ref>
• 43A2<ref name="G96Manual"/>

See also

• GROMOS
• Ascalaph Designer
• Comparison of software for molecular mechanics modeling
• Comparison of force field implementations

External links

• Template:Official website