Force fields GROMOS

Gronigen molecular simulation (GROMOS) is the name of both a force field and the program incorporating that force field. The GROMOS force field is popular for predicting the dynamical motion of molecules and bulk liquids. It is... 

Oostenbrink, C. Villa, A. Mark, A. E van Gunsteren, W. F., A biomolecular force field based on the free enthalpy of hydration and solvation the Gromos force-field parameter sets 53A5 and 53A6., J. Comput. Chem. Oct 2004, 25, 1656-1676. 

Tapia O, Velasquez I (1997) Molecular Dynamics Simulations of DNA with Protein s Consistent GROMOS Force Field and the Role of Counterions Symmetry, J Am Chem Soc, 119 5934... 

Computed with the (aug)Kx -pVTZ basis set and the GROMOS force field. Activation enthalpy. ... 

Molecular Dynamics Simulation of the Proline Conformational Equilibrium and Dynamics in Antamanide Using the GROMOS Force Field. 

Gradient Extremal (GE), 338 Gradient norm minimization, 333 Gradient of a function, 238 Greens function, 257 GROMOS force field, 40 Gross atomic charge, 218... 

R. D. Lins and P. H. Hiinenberger, A new GROMOS force field for hexopyranose-based carbohydrates, J. Comput. Chem., 26 (2005) 1400-1412. 

The hybrid scheme used by us has been described in detail (1). Therefore, only a short summary is given here. The system is divided into a primary (QM) part treated quantum-chemically and the environment treated by a force field (MM part). For the QM part, a semi-empirical calculation is carried out. We have used the MOPAC program (2) for this task and have, consequently, employed all NDDO methods (MNDO, AMI, PM3) in the course of our work. The interactions among atoms of the MM part are described entirely by a classical force field. They are evaluated using die GROMOS87 program (3), and the GROMOS force field or close variations of it were used in our work. 

Stephenson G 1973 Mathematical Methods for Science Students. London, Longman Swaminathan S, G Ravishanker and D L Beveridge 1991. Molecular Dynamics of B-DNA Including Water and Counterions - A 140-ps Trajectory for d(CGCGAATTCGCG) Based on the Gromos Force Field Journal of the American Chemical Society 113-5027-5040... 

The first important dynamic CyD studies published in 1987 and 1988 were the result of cooperation by the theoreticians van Gunsteren and Koehler with the X-ray specialist Saenger [98, 99, 100, 101, 102]. The aim of these studies was twofold on the one hand, they served the development of the GROMOS force field [103] while on the other they had to show that DSs for such complicated systems as CyDs were feasible. Starting from the experimental structures, these simulations of 15 or 20 ps, very short by today s standards, are of historical interest only. Similarly, the work by Mark et al. [104] of 1994 on free perturbation calculations was mainly devoted to the development of the method. 

Van der Waals interactions are proportional to 1/Rfj at large distances and so are short range. A van der Waals cutoff distance of 8 A is typically used and was believed to produce little error. However, molecular-dynamics simulations of liquid alkanes using the GROMOS force field found that the enthalpies of vaporization and the vapor pressures changed very substantially when the van der Waals cutoff distance was varied within the range 8 to 14 A, and so a van der Waals cutoff radius of 16 A is much more justifiable than the traditional one of 8 A [X. Daura et al., J. Comput. Chem., 19, 535 (1998)]. 

The structure, conformation and intramolecular hydrogen bonds of crystalline and aqueous sucrose have been discussed in detail. Evidence for a transient inter-residue hydrogen bond in aqueous sucrose (0-2- -H O-T) has been discovered by ROESY spectroscopy imder supercooled conditions.Combined use of high resolution NMR techniques and dynamics simulations furnished a new model for the dynamical conformational behaviour of sucrose in water in which internal motions occur at the same rate as overall tumbling. A GROMOS force field analysis, modified to include a potential energy term for the fxo-anomeric effect, has been assessed for efficiency by application to a conformational analysis of a-maltose. ... 

Horta, B. A. C., P. F. J. Fuchs, W. F. van Gunsteren, and P. H. Hunenberger. 2011. New interaction parameters for oxygen compounds in the GROMOS force field Improved pure-liquid and solvation properties for alcohols, ethers, aldehydes, ketones, carboxylic acids, and esters. Journal of Chemical Theory and Computation. 7, 1016. 

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