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Molecular mechanics and dynamics of biomolecules using a solvent continuum model
Author(s) -
Fogolari F.,
Esposito G.,
Viglino P.,
Molinari H.
Publication year - 2001
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.1134
Subject(s) - molecular dynamics , solvation , implicit solvation , statistical physics , molecular mechanics , solvent models , polar , computation , continuum mechanics , chemistry , biomolecule , computational chemistry , solvent , physics , thermodynamics , computer science , materials science , nanotechnology , quantum mechanics , algorithm , organic chemistry
An easy implementation of molecular mechanics and molecular dynamics simulation using a continuum solvent model is presented that is particularly suitable for biomolecular simulations. The computation of solvation forces is made using the linear Poisson–Boltzmann equation (polar contribution) and the solvent‐accessible surface area approach (nonpolar contribution). The feasibility of the methodology is demonstrated on a small protein and a small DNA hairpin. Although the parameters employed in this model must be refined to gain reliability, the performance of the method, with a standard choice of parameters, is comparable with results obtained by explicit water simulations. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1830–1842, 2001