MOLECULAR-DYNAMICS STUDIES OF SOLVATED POLYPEPTIDES - WHY THE CUTOFF SCHEME DOES NOT WORK

While atom-atom pair correlations are insensitive to cut-off variations, it is found that orientational correlation functions are central for the analysis and understanding of the consequences of an incorrect treatment of long-range Coulomb forces in molecular dynamics simulations of solvated polypeptides. In particular, the mutual orientation between a water dipole and its joining vector to an ion as well as the alignment of two water dipoles are sensitive probes, because their qualitative behaviour can be analysed on the basis of an effective interaction derived from dielectric continuum theory. The use of a simple spherical truncation scheme introduces artificial long-range correlations and even distorts short-range order. While these spurious artifacts disappear when using the Ewald summation technique, they are responsible for the rapid unfolding of a helical peptide during cut-off simulations. Therefore the cut-off scheme cannot be recommended for simulations of solvated biomolecules.