Normal mode analysis using the driven molecular dynamics method. II. An application to biological macromolecules.
The driven molecular-dynamics (DMD) method, recently proposed by Bowman, Zhang, and Brown [J. Chem. Phys. 119, 646 (2003)], has been implemented into the TINKER molecular modeling program package. The DMD method yields frequencies and normal modes without evaluation of the Hessian matrix. It employs an external harmonic driving term that can be used to scan the spectrum and determine resonant absorptions. The molecular motions, induced by driving at resonant frequencies, correspond to the normal-mode vibrations. In the current work we apply the method to a 20-residue protein, Trp-cage, that has been reported by Neidigh, Fesinmeyer, and Andersen [Nature Struct. Biol. 9, 425 (2002)]. The structural and dynamical properties of this molecule, such as B-factors, root-mean square fluctuations, anisotropies, vibrational entropy, and cross-correlations coefficients, are calculated using the DMD method. The results are in very good agreement with ones calculated using standard normal-mode analysis method. Thus, the DMD method provides a viable alternative to the standard Hessian-based method and has considerable potential for the study of large systems, where the Hessian-based method is not feasible.
Kaledin
Martina
M
Cherry L. Emerson Center for Scientific Computation, Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA.
Brown
Alex
A
Kaledin
Alexey L
AL
Bowman
Joel M
JM
D000465:Algorithms; D001704:Biopolymers / Q000737:chemistry*; D003198:Computer Simulation; D007700:Kinetics; D046911:Macromolecular Substances / Q000737:chemistry*; D008956:Models, Chemical; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*
D001704:Biopolymers; D046911:Macromolecular Substances; D010455:Peptides; C508725:Trp-cage peptide