Boundary condition effects on the dynamic and electric properties of hydration layers.
Water solvation has a central role in several biochemical processes ranging from protein folding to biomolecular recognition and enzyme catalysis. Because of its importance, the structure and dynamics of hydration layers around biological macromolecules have been the targets of a great number of experimental and computational studies. In the present contribution, we have investigated the effects of periodic boundary conditions (PBCs), as used in conjunction with molecular dynamics (MD) simulations, on the dynamic and electric properties of water layers. In particular, we have systematically performed MD simulations of neat water and biomolecules in aqueous solutions by imposing a different external dielectric constant, a generally overlooked parameter in PBC simulations. The effect of the system size has also been addressed. Overall, our results consistently indicate that the dipole moment properties of water layers, and specifically the dipole moment fluctuations and the reorientational correlation functions, can be sensitive to the choice of the external boundary conditions, whereas other molecular properties, such as the self-diffusion coefficient and the reorientational relaxation times, are not affected. We think that our investigation may help to assess appropriate simulation conditions for modeling the aqueous environment of relevant biochemical systems and processes.
†Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.
Balasubramanian
B
Chandramouli
†Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.
Costantino
C
Zazza
†Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.|‡Istituto Nazionale di Fisica Nucleare (INFN) Sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy.
Giordano
G
Mancini
†Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.|‡Istituto Nazionale di Fisica Nucleare (INFN) Sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy.
Giuseppe
G
Brancato
D000409:Alanine / Q000737:chemistry; D003300:Copper / Q000737:chemistry; D004058:Diffusion; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry; D010970:Plastocyanin / Q000737:chemistry; D012399:Rotation; D012997:Solvents / Q000737:chemistry*; D014867:Water / Q000737:chemistry*
D010455:Peptides; D012997:Solvents; D014867:Water; D003300:Copper; D010970:Plastocyanin; D000409:Alanine