ENCORE: Software for Quantitative Ensemble Comparison
Fig 6
Effect of sparsifying the simulation data.
We evaluated the robustness of the calculated similarity scores when decreasing the ensemble size. In particular, we took 8192 (213) frames separated by 1ns from a simulation of GB3 using Amber ff03 as a reference and created subensembles of various sizes by iteratively removing every second frame. We subsequently calculated the three different similarity scores between the full ensemble and the various subensembles that contained between 128 and 4096 frames. The results show that even when only every 16th frame is retained the pairwise similarity is very high (divergence close to zero), demonstrating both the robustness of the calculations and that such sparsification likely is an efficient way of improving computational efficiency in practice.