Journal of Physical Chemistry B, Vol.104, No.47, 11342-11348, 2000
Methyl motional parameters in crystalline L-alanine: Molecular dynamics simulation and NMR
The correlation time for side-chain methyl reorientation in crystalline L-[beta-H-2(3)]alanine is calculated from molecular dynamics (MD) simulations and compared with NMR measurements. Correlation times for methyl reorientation may be a sensitive measure of packing in proteins, and characterizing the motions of sidechains is of interest for protein folding. Converged correlation functions were obtained by averaging over all side-chain methyls in the primary cell of MD simulations with periodic boundary conditions. When corrected for neglect of quantum mechanical tunneling, the correlation times from simulation are in excellent agreement with those from NMR, but this difference may not be significant. A torsional parameter in the CHARMM22 force field was reduced on the basis of ab initio calculations for use in the simulations, and the agreement between MD and NMR correlation times confirm that this was correct.