Paper Citing NAMD - Abstract
Nayar, Divya; Agarwal, Manish; Chakravarty, Charusita
Comparison of Tetrahedral Order, Liquid State Anomalies, and Hydration Behavior of mTIP3P and TIP4P Water Models
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3354-3367, OCT 2011
The relationship between local tetrahedral order, tagged particle potential energy, and coordination number is studied for mTIP3P and TIP4P models of water in the bulk as well as in the neighborhood of a small peptide. The tendency of water molecules with different binding or tagged particle potential energies to occupy environments with different degrees of disorder can be effectively illustrated by constructing tetrahedral order distributions and corresponding entropy metrics conditional on restricted ranges of local binding energy. At the state point corresponding to the onset of the density anomaly, the correlation between tetrahedral entropy versus tagged potential energy is strong and virtually identical for mTIP3P and TIP4P. In TIP4P, this correlation is retained up to temperatures as high as 300 K, while it is lost by 250 K in mTIP3P. In the 250-300 K regime that is important for biomolecular simulations, mTIP3P behaves essentially as a simple liquid while TIP4P shows the density and related anomalies characteristic of water. We also study the number of water molecules, the tetrahedral order, and the tagged molecule potential energies for water molecules as a function of the distance from the peptide for the 16-residue /3-hairpin fragment of 2GB I in mTIP3P and TIP4P solvents. The hydration shell coordination profiles (n(r)) of the number of water molecules are almost identical in the two solvents, but the radial variation in the local energies and local order show significant differences. The residue-wise variation in the tagged potential energy of water molecules within the first hydration shell is qualitatively similar in the two models. A comparison of the tetrahedral order distributions of water molecules lying at different distances from the biomolecular solute shows that the perturbation in the local tetrahedral order distributions of the bulk solvent due to the presence of the solute is marginal. Thus, in the 250-300 K regime, the mTIP3P and TIP4P water models show qualitatively different behavior in terms of the relationship between tetrahedral order and local energy, but as solvents in the neighborhood of a biornolecular solute, the differences between the two models are only quantitative and not qualitative.
