Elastic bag model for molecular dynamics simulations of solvated systems: application to liquid water and solvated peptides.
The fluctuating elastic boundary (FEB) model for molecular dynamics has recently been developed and validated through simulations of liquid argon. In the FEB model, a flexible boundary which consists of particles connected by springs is used to confine the solvated system, thereby eliminating the need for periodic boundary conditions. In this study, we extend this model to the simulation of bulk water and solvated alanine dipeptide. Both the confining potential and boundary particle interaction functions are modified to preserve the structural integrity of the boundary and prevent the leakage of the solute-solvent system through the boundary. A broad spectrum of structural and dynamic properties of liquid water are computed and compared with those obtained from conventional periodic boundary condition simulations. The applicability of the model to biomolecular simulations is investigated through the analysis of conformational population distribution of solvated alanine dipeptide. In most cases we find remarkable agreement between the two simulation approaches.
Li
Yuhui
Y
Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, USA.
Krilov
Goran
G
Berne
B J
BJ
D006860:Hydrogen Bonding; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry; D014867:Water / Q000737:chemistry*
D010455:Peptides; D012997:Solvents; D014867:Water