A series of normal mode analyses of bovine pancreatic trypsin mhibitor (BPTI) has been performed. The results of modifying the long-range truncation of electrostatics, reducing the conformational space of the system (reduced basis normal mode analysis), and using different parameter sets and models for the potential function are reported. Both explicit (904 atoms) and polar hydrogen (580 atoms) representations of BPTI were examined and produced nearly identical normal mode vectors but slightly modified vibrational frequencies. The truncation methods-no cutoff, shift, and switch-were examined, and the use of a short switching function was found to alter harmonic motion greatly. A table relating the different cutoff methods to several previously published frequencies for BPTI indicates that the diversity of published lowest frequencies is due to the use of different electrostatic models rather than to inherent differences in the models or energy parameters. Examining reduced basis results demonstrates that a dihedral basis yields similar normal mode vectors, though the vibrational frequencies are shifted to higher values. The analysis of BPTI harmonic dynamics using a spherical harmonic reduced basis set yields significantly altered dynamics, indicating that BPTI is not well represented as a homogeneous object at low temperatures. 0 1995 by John Wiley & Sons, Inc.' monic analysis in full and reduced Cartesian basis were developed. Using a mass-weighted form of the second derivative matrix of the potential, the normal modes are obtained through diagonalization. The eigenvectors correspond to the massperform mode and quasiharm weighted normal mode displacements, and the eigenvalues are proportional to the square of fiequencies. F~~ small systems this can be performed by straightforward procedures. The treatment be-* Author to whom all correspondence should be addressed.