Force Fields and Molecular Dynamics Simulations

Macromolecular Force Fields and Molecular Dynamics Simulations 

The most significant advantage offered by macromolecular force fields, such as AMBER,108.109 CHARMm,no and GROMOS,iii.n2 over those already discussed is suitability for performing MD simulations. This feature, when combined with the option to treat solvent explicitly under periodic boundary conditions, leads to a realistic approach to simulating the properties of the oligosaccharides in solution. Moreover, physical observables such as solvent RDFs may be used as criteria to determine the accuracy of the treatment 

Also in 1990, Homans added a torsional term for the exo-anomeric effect to Brady s CHARAlm-type parameters and incorporated them into AMBER. As with more recent versions of HSEA, Homans exo-anomeric parameters were chosen to reproduce ab initio rotational energies computed at the HF/6-31G level for dimethoxymethane (Eqs. [12] and [13]).  

The Homans parameters have been used for both solvated and in vacuo 3 i3 simulations. In a recent study of a tetrasaccharide model for the blood group determinant Lewis-X (P-D-Gal(l-4)[a-L-Fuc(l-3)]p-D-GlcNAc(l-3)p-D-Gal) (7), Homans and Forster proposed a protocol for carbohydrate conformational analysis. o Their protocol was composed of the six components summarized in Table 1. 

In vacuo minimization with interproton distance restraints 

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