Paper Citing NAMD - Abstract
Cerutti, David S.; Freddolino, Peter L.; Duke, Robert E., Jr.; Case, David A.
Simulations of a Protein Crystal with a High Resolution X-ray Structure: Evaluation of Force Fields and Water Models
JOURNAL OF PHYSICAL CHEMISTRY B, 114:12811-12824, OCT 14 2010
We use classical molecular dynamics and 16 combinations of force fields and water models to simulate a protein crystal observed by room-temperature X-ray diffraction. The high resolution of the diffraction data (0.96 angstrom) and the simplicity of the crystallization solution (nearly pure water) make it possible to attribute any inconsistencies between the crystal structure and our simulations to artifacts of the models rather than inadequate representation of the crystal environment or uncertainty in the experiment. All simulations were extended for 100 its of production dynamics, permitting some long-time scale artifacts of each model to emerge. The most noticeable effect of these artifacts is a model-dependent drift in the unit cell dimensions, which can become as large as 5% in certain force fields; the underlying cause is the replacement of native crystallographic contacts with non-native ones, which can occur with heterogeneity (loss of crystallographic symmetry) in simulations with some force fields. We find that the AMBER FF99SB force field maintains a lattice structure nearest that seen in the X-ray data, and produces the most realistic atomic fluctuations (by comparison to crystallographic B-factors) of all the models tested. We find that the choice of water model has a minor effect in comparison to the choice of protein model. We also identify a number of artifacts that occur throughout all of the simulations: excessive formation of hydrogen bonds or salt bridges between polar groups and loss of hydrophobic interactions. This study is intended as a foundation for future work that will identify individual parameters in each molecular model that can he modified to improve their representations of protein structure and thermodynamics.
