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Impressum
(c) 2002 BMO

"Linearly Scaling and Almost Hamiltonian Dielectric Continuum Molecular Dynamics Simulations through Fast Multipole Expansions"
Konstantin Lorenzen, Gerald Mathias, and Paul Tavan
J. Chem. Phys. 143, 184114 (2015).


Abstract:
Hamiltonian Dielectric Solvent (HADES) is a recent method (Bauer et al., J. Chem. Phys. 2014, 140, 104103), which enables atomistic Hamiltonian molecular dynamics (MD) simulations of peptides and proteins in dielectric solvent continua. Such simulations become rapidly impractical for large proteins, because the computational effort of HADES scales quadratically with the number N of atoms. If one tries to achieve linear scaling by applying a fast multipole method (FMM) to the computation of the HADES electrostatics, the Hamiltonian character (conservation of total energy, linear, and angular momenta) may get lost. Here we show that the Hamiltonian character of HADES can be almost completely preserved, if the structure-adapted fast multipole method (SAMM) as recently redesigned by Lorenzen et al. (J. Chem. Theory. Comput. 2014, 10, 3244-3259) is suitably extended and is chosen as the FMM module. By this extension the HADES/SAMM forces become exact gradients of the HADES/SAMM energy. Their translational and rotational invariance then guarantees (within the limits of numerical accuracy) the exact conservation of the linear and angular momenta. Also the total energy is essentially conserved - up to residual algorithmic noise, which is caused by the periodically repeated SAMM interaction list updates. These updates entail very small temporal discontinuities of the force description, because the employed SAMM approximations represent deliberately balanced compromises between accuracy and efficiency. The energy-gradient corrected version of SAMM can also be applied, of course, to MD simulations of all-atom solvent-solute systems enclosed by periodic boundary conditions. However, as we demonstrate in passing, this choice does not offer any serious advantages.

BMO authors (in alphabetic order):
Konstantin Lorenzen
Gerald Mathias
Paul Tavan

Assoziierte Projekte:
Computation of structure, electrostatics, and conformational dynamics of PrPC induced by binding of Cu(II)
Long-range electrostatics in molecular dynamics simulations


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Letzte Änderung: 2016-09-14 13:34