FLUCTUATION AND CROSS-CORRELATION ANALYSIS OF PROTEIN MOTIONS OBSERVED IN NANOSECOND MOLECULAR-DYNAMICS SIMULATIONS

Long range positive correlations in the internal atomic motions have b een observed in molecular dynamics simulations of the bovine pancreati c trypsin inhibitor. Since the results depend, on the removal of overa ll translation and rotation (which is not unique), some care is requir ed. It is pointed out that original use of all of the C-alpha atoms as a frame of reference is more appropriate than the selection of a parti cular subset. The former comes closest to reflecting the zero rotation condition in a normal mode analysis, which also shows the existence o f long range correlations. (C) 1996 Academic Press Limited