Paper Citing NAMD - Abstract
Burden, Conrad J.; Oakley, Aaron J.
Anisotropic atomic motions in high-resolution protein crystallography molecular dynamics simulations
PHYSICAL BIOLOGY, 4:79-90, JUN 2007
Molecular dynamics (MD) simulations using empirical force fields are popular for the study of proteins. In this work, we compare anisotropic atomic fluctuations in nanosecond-timescale MD simulations with those observed in an ultra-high-resolution crystal structure of crambin. In order to make our comparisons, we have developed a compact graphical technique for assessing agreement between spatial atomic distributions determined by MD simulations and observed anisotropic temperature factors.
