Consistent principal component modes from molecular dynamics simulations of proteins

RODRIGO COSIO PEREZ; JULIANA PALMA; GUSTAVO PIERDOMINICI-SOTTILE

JOURNAL OF CHEMICAL INFORMATION AND MODELING

AMER CHEMICAL SOC

Lugar: Washington; Año: 2017 vol. 57 p. 826 - 834

1549-9596

Principal component analysis is a technique widely used for studying the movements of proteins using data collected from molecular dynamics simulations. In spite of its extensive use the technique has a serious drawback: equivalent simulations do not afford the same PC-modes. In this article we show that concatenating equivalent trajectories and calculatingthe PC-modes from the concatenated one significantly enhances the reproducibility of the results. Moreover, the consistency of the modes can be systematically improved by adding more individual trajectories to the concatenated one.