Fig. 3: Scaling in number of eigenmodes in Chebyshev-filtered thick restart Lanczos method.
From: Scalable computation of anisotropic vibrations for large macromolecular assemblies
Up to 1000 or slightly more eigenpairs were calculated using our INCHING-CTRLM-HalfSparse implementation of the Chebyshev-filtered Thick Restart Lanczos Method with radius of interaction \({R}_{C}\) = 8Å. The coloring of the lines, as shown in the color bar, refers to the number of atoms in the system. a Run time to complete until the indexed eigenvalue (b) optimized polynomial degrees involved in calculating the indexed eigenvalue. c Peak memory consumed when calculating the spectrum slice containing the indexed eigenvalue. d Residual error in each of the eigenvalues. e Mapping of the lowest 224 eigenvalues in batches of 28 eigenvectors when low- and band-pass Chebyshev filters were applied to the HIV capsid system (PDBID: 3J3Q) without coarse-graining. Colors of the points indicate eigenvalues resolved in different batches. Source data are provided as a Source Data file.
