Fluctuation and cross correlation analysis of protein motions observed in nanosecond molecular dynamics simulations

Long range positive correlations in the internal atomic motions have been observed in molecular dynamics simulations of the bovine pancreatic trypsin inhibitor. Since the results depend, on the removal of overall translation and rotation (which is not unique), some care is required. It is pointed out that original use of all of the C-alpha atoms asa frame of reference is more appropriate than the selection of a particular subset. The former comes closest to reflecting the zero rotation condition in a normal mode analysis, which also shows the existence of long range correlations. (C) 1996 Academic Press Limited