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Nonperiodic boundary conditions for solvated systems.
Journal article

Nonperiodic boundary conditions for solvated systems.

  • Petraglio 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 M
  • Parrinello M
  • 2005-08-13
Published in:
  • The Journal of chemical physics. - 2005
Acetonitriles
Computer Simulation
Models, Chemical
Peptides
Solutions
Surface Properties
Water
English 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.
Language
  • English
Open access status
closed
Identifiers
Persistent URL
https://folia.unifr.ch/global/documents/207855
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