Computational Performance

Here we want to document that FAMUSAMM actually provides an enhanced computational efficiency both as compared to SAMM as well as to the reference method which is characterized by exact evaluation of the Coulomb sum. To that aim we have carried out a series of test simulations for systems of varying size ranging from 500 to 40,000 atoms. We used the sequential version of EGO_VIII. All simulations were executed on a DEC-ALPHA 3300L (175 MHz) workstation equipped with 96 MB RAM. Figure 3 shows that the average computation time required for one MD integration step scales linearly with system size for systems comprising more than about 1,000 atoms.

  

Figure: Average computation time for one step using EGO_VIII on a DEC-Alpha 3300L workstation (175 MHz) for simulation systems of varying size. The insets show some of the protein-water systems used for the benchmark simulations.

For large systems comprising 36,000 atoms FAMUSAMM performs four times faster than SAMM and as fast as a cut-off scheme with a $10\,$Å cut-off distance while completely avoiding truncation artifacts. Here, the speed-up with respect to SAMM is essentially achieved by the multiple-time-step extrapolation of local Taylor expansions in the outer distance classes. For this system FAMUSAMM executes by a factor of 60 faster than explicit evaluation of the Coulomb sum. The subsequent Section describes, as a sample application of FAMUSAMM, the study of a ligand-receptor unbinding process.