Nonperiodic boundary conditions for solvated systems.
The simulation of charged and/or strongly polar solutes represents a challenge for standard molecular-dynamics techniques. The use of periodic boundary conditions (PBCs) leads to artifacts due to the interaction between two replicas in the presence of the long-range Coulomb forces. A way to avoid these problems is the use of nonperiodic boundary conditions. A possible realization is to consider a finite system, a sphere, embedded in a reaction field described by the method of the images. In the present work the modified image approximation has been implemented in a molecular-dynamics code and optimized for the use of two standard solvents, water and acetonitrile. The methodology has then been applied to investigate the conformational changes in water-solvated alanine dipeptide. The free-energy surface calculated with this method is comparable to that obtained with PBC.
Petraglio
Gabriele
G
Computational Science, Department of Chemistry and Applied Biosciences Eidgenössische Technische Hochshule Zurich, USI Campus, via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland. gpetraglio@phys.chem.ethz.ch
Ceccarelli
Matteo
M
Parrinello
Michele
M
D000097:Acetonitriles / Q000737:chemistry*; D003198:Computer Simulation; D008956:Models, Chemical; D010455:Peptides / Q000737:chemistry*; D012996:Solutions / Q000737:chemistry; D013499:Surface Properties; D014867:Water / Q000737:chemistry*
D000097:Acetonitriles; D010455:Peptides; D012996:Solutions; D014867:Water; C032159:acetonitrile