The presence of Ewald artifacts in a molecular dynamics simulation of a zwitterionic tetrapeptide in aqueous solution has been investigated. Both equilibrium and dynamical aspects of the rotational behavior of the peptide were examined. The equilibrium distribution of rotational states obtained from a 10 ns simulation were consistent, within statistical errors, with a random distribution free from Ewald artifacts. The rotational dynamics of the peptide was observed to obey simple Debye diffusion with a rotational diffusion rate in agreement with that predicted by a simple rotational diffusion model assuming no substantial long-lived water hydration shell. These results suggest that rotational Ewald artifacts will be negligible for small biomolecular simulations in solvents with high relative permittivities. The data support the results obtained from a previous study of simpler model systems.
ASJC Scopus subject areas
- Physical and Theoretical Chemistry
- Surfaces, Coatings and Films
- Materials Chemistry