The _sims folders contain the molecular dynamics trajectories for the two homodimers and the heterodimers in gromcas format.

Within each folder, the index.ndx file in the top directory can be read by gromacs specifies groups of residues in the homodimers (such as the beta sandwich etc.).

Within the folders are two gromacs .tpl topology files. One (just called relax2.tpr describes the topology after a brief pre-equilibration 	run. The other _2000.tpr describes the topology for the 2 usec simulation. The .xtc file contains the actual trajectory in the gromacs .xtc format. 

The other folders contain gromacs output text files that were used to generate panels B-E.