Paper Citing NAMD - Abstract
Glass, Dennis C.; Krishnan, Marimuthu; Nutt, David R.; Smith, Jeremy C.
Temperature Dependence of Protein Dynamics Simulated with Three Different Water Models
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:1390-1400, APR 2010
The effect of variation of the water model on the tempera lure dependence of protein and hydration water dynamics is examined by performing molecular dynamics simulations of myoglobin with the TIP3P, TIP4P, and TIP5P water models and tie CHARMM protein force field at temperatures between 20 and 300 K. The atomic mean-square displacements, solvent reorientational relaxation times, pair angular correlations between surface water molecules, and time-averaged structures of the protein are all found to be similar, and the protein dynamical transition is described almost indistinguishably for the three water potentials. The results provide evidence that for some purposes changing the water model in protein simulations without a loss of accuracy may be possible.
