Principal Component Analysis for Molecular Dynamics Simulation of the Crystal Phase Transition

Perturbational formulation of principal component analysis in molecular dynamics simulation.

Conformational fluctuations of a molecule are important to its function since such intrinsic fluctuations enable the molecule to respond to the external environmental perturbations. For extracting large conformational fluctuations, which predict the primary conformational change by the perturbation, principal component analysis (PCA) has been used in molecular dynamics simulations. However, sev...

Molecular-dynamics simulation of the structural phase transition in Rb2CaCl4.

Dihedral angle principal component analysis of molecular dynamics simulations.

It has recently been suggested by Mu et al. [Proteins 58, 45 (2005)] to use backbone dihedral angles instead of Cartesian coordinates in a principal component analysis of molecular dynamics simulations. Dihedral angles may be advantageous because internal coordinates naturally provide a correct separation of internal and overall motion, which was found to be essential for the construction and i...

Molecular dynamics of apo-adenylate kinase: a principal component analysis.

Adenylate kinase from E. coli (AKE) is studied with molecular dynamics. AKE undergoes large-scale motions of its Lid and AMP-binding domains when its open form closes over its substrates, AMP and Mg2+-ATP. The third domain, the Core, is relatively stable during closing. The resulting trajectory is analyzed with a principal component analysis method that decomposes the atom motions into modes or...

Superprotonic phase transition of CsHSO4: A molecular dynamics simulation study

Calum R. I. Chisholm,1 Yun Hee Jang,2 Sossina M. Haile,1 and William A. Goddard III2,* 1Department of Materials Science, California Institute of Technology, Pasadena, California 91125, USA 2Materials and Process Simulation Center, Beckman Institute (139-74), California Institute of Technology, Pasadena, California 91125, USA Received 14 July 2004; revised manuscript received 21 January 2005; pu...