Dynamic Indices

For most analyses we use index files containing atom numbers, e.g. the atoms used for the RDF calculation. Since we want to bring this to a new level of abstraction we'd also need something like "dynamic indices", such that one at each step determines, e.g. which are the oxygen atoms in a protein. This is necessary when the number of atoms is dynamic as well.

As an example, consider the aggregation of lipids into a micelle during MD simulations. The number of lipids in the micelle is not constant, and (in equilibrium) their molecular identity is not the same. One may be interested in calculating the minimal distance between the micelle and other molecules, its radius of gyration, RDF between molecules in the micelles etc., which cannot be performed with fixed number of atoms in the index file.

One approach to deal with this issue involves merging make_ndx functionality within all analysis tools.

Alternatively, a single tool may be used which has the ability to dynamically create an index for each frame which is read (e.g. by clustering as in g_clustsize or by minimal distance to a group as in g_mindist) and then be able to run a series of calculations using this index: minimal distance (to one or more groups), RDF, radius of gyration, h-bonds, secondary structure etc. This can be a follow up project once an Analysis Library is made.