Comparing molecular simulations using ENCORE.

<p>We used ENCORE to calculate the similarity between seven molecular dynamics simulations of (A, B) protein G and (C) ubiquitin. (A) The plots show the pairwise similarity between the seven ensembles computed using the three different ensemble comparison methods. (B) Using the similarities calculated by the CES method as an example, a tree-preserving embedding method was used to represent the ensembles in two-dimensions. In this plot, the distance between pairs of ensembles mimics (to the extent possible in two dimensions) the similarity between different ensembles. In agreement with the pairwise similarities, three pairs of ensembles (CHARMM22*/CHARMM27, ff99SB-ILDN/ff99SB*-ILDN, and ff03/ff03*) are located relatively close to one another, in line with the similar origins of each pair of force fields. (C) We performed similar calculations on seven ubiquitin simulations, again using the CES method as an example and projecting the similarities into two-dimensions. A similar organization is found for the different ensembles for both proteins, as is also evident from directly comparing the matrices of ensemble similarities. Note that in the projections, the axes have no direct physical meaning beyond their scale, which are determined so that the distance in the projections are close to the calculated <i>D</i>_JS. Note also that since these distances are invariant to rotations, translations and inversions of the projections, it is the relative positions in the two plots that should be compared.