"CULGI works with the petroleum industry on modeling applications such as asphaltene precipitation, oil emulsification and lubrication. In all cases we use a multi-scaled approach to combine molecular structure with thermodynamics. The picture shows a detailed background of alkanes, and a coarse-grained molecule in the foreground."
One of the key elements of multi-scale modelling is the transition from one level of detail to another. The picture shows the same simple alkane described in two ways: in the familiar atomistic way as used in molecular mechanics, and as in a CULGI coarse-grained model, where one 'bead' in the chain represents three carbon atoms and the associated hydrogens. The center of each bead is the center of mass of the atom group that it represents.
An actual coarse-grained simulation will require parameters for these coarse-grained molecules, such as bond lengths for the distance between beads in a chain. One way of deriving some of the necessary parameters is by doing the kind of mapping described here, for many realistic configurations of the atomistic system (for example, the trajectory of a molecular dynamics simulation). Analyzing the resulting coarse-grained configurations then gives distributions of bond lengths and bond angles, which can be used to derive bond and angle parameters for the coarse-grained model.
Paul Becherer, Development Scientist, Culgi B.V. Leiden, The Netherlands