Given a reliable and accurate force field, biomolecular simulations are capable to provide average properties, distributions and the time evolution behavior of any defined thermodynamical quantity. This is of particular interest when treating intrinsic highly flexible systems such as carbohydrates and membranes, as experimental measurements provide only average values. Sampling of the appropriate phase space depends on the spatial resolution, time scale and degrees of freedom. Computer time and/or scalability limitations make the study of some biological phenomena not always at reach. Coarse-grained force fields have been developed towards this end. These force fields map a group of atoms into a bead decreasing the total number of particle in a system at the expense of some chemical details. Degrees of freedom are dramatically reduced and energy barriers smoothed, granting the use of large time steps and a more efficient sampling. However, backwards compatibility with a finer grained force field has not been a common goal in the community. Using a bottom-up approach, experimental data and free energy calculations for model compounds have been used to develop consistent GROMOS-compatible fine- and coarse-grained force fields for carbohydrates. The new version of the atomistic force field exhibits improved puckering distributions and it is fully compatible with the GROMOS force field for proteins and lipids, allowing for simulations of glycoproteins and lipoglycam membranes and moieties. Its four-bead/residue coarse-grained counterpart displays point charges and easy inverse mapping between alpha and beta anomers. Validation is showcased for amylose V, A and alpha-, beta- and gamma-cyclodextrins. Moreover, solvation quantities are properly described for mixed coarse-grained solute/fine grained solvent.

Development of fine- and coarse-grained carbohydrate force fields: When one size fits all

248th National Meeting (2014)

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