Lennard-Jonesium (“lennard-jones-ium”) 38 requires enhanced sampling to visit the entire space spanned by these variables because it is not ergodic on the timescale of the simulation. Berendsen et al. extracted the essential dynamics of protein fluctuations into modes that make excellent choices for these variables, which are obtained through dimensional reduction of trajectories in molecular dynamics. An “intrinsic” choice of these variables traces the unique minimum energy path through 3N-minus-6-dimensional configuration space. The synchronous transit method finds points where the derivative of the Gibbs free energy with respect to these variables is zero on a PES (“P-E-S”). These variables are the x-axis on plots with local maxima at transition states. For 10 points, name these variables chosen to represent changes in structure during a reaction. ■END■
ANSWER: reaction coordinates [or collective variables; accept intrinsic reaction coordinates or geometric coordinates or order parameters; prompt on parameters; prompt on atomic or nuclear positions, bond angles, dihedral angles, or bond lengths by asking “they are part of what broader set of variables?”]
<Chemistry>
= Average correct buzz position