AG Tavan - Projects

LMU München
Fakultät für Physik



(c) 2002 BMO

Long-range electrostatics in molecular dynamics simulations
(Protein dynamics in their native environment)

Development of a continuum electrostatics approach allowing to calculate the electrostatic interactions between the (partial) charges of an arbitrary shaped solute and a dielectric and ionic solvent continuum.

Combination of periodic boundary conditions with the fast structure-adapted multipole method (SAMM), and with the Kirkwood reaction field to generate an efficient algorithm for simulating protein solvent systems.

Implementation of these features in our molecular dynamics package EGO MMII

Previous coworkers:  Bernhard Egwolf
Markus Eichinger
Helmut Grubmüller
Helmut Heller
Gerald Mathias
Christoph Niedermeier
Martina Stork
Paul Tavan

Publications:  "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).

"Exploring Hamiltonian Dielectric Solvent Molecular Dynamics"
S. Bauer, P. Tavan, G. Mathias
Chem. Phys. Lett. 612 20-24 (2014).

"Including the Dispersion Attraction into Structure-Adapted Fast Multipole Expansions for MD Simulations"
Konstantin Lorenzen, Christoph Wichmann and Paul Tavan
J. Chem. Theory. Comput. 10, 3244-3259 (2014).

"Electrostatics of proteins in dielectric solvent continua. II. Hamiltonian reaction field dynamics."
Sebastian Bauer, Paul Tavan, and Gerald Mathias
J. Chem. Phys. 140, 104103 (2014)

"Electrostatics of proteins in dielectric solvent continua. I. An accurate and efficient reaction field description."
Sebastian Bauer, Gerald Mathias, and Paul Tavan
J. Chem. Phys. 140, 104102 (2014).

"Optimizing the accuracy and efficiency of fast hierarchical multipole expansions for MD simulations"
Konstantin Lorenzen, Magnus Schwörer, Philipp Tröster, Simon Mates, and Paul Tavan
J. Chem. Theory Comput. 8, 3628-3636 (2012).

"Molecular dynamics simulations of proteins and peptides: Problems, achievements, and perspectives"
Paul Tavan, Heiko Carstens, and Gerald Mathias
In: Protein Folding Handbook. Part I. J. Buchner and T. Kiefhaber (Eds.), Wiley-VCH, Weinheim (2005), 1170-1195.

"Elektrostatische Wechselwirkungen in komplexen Flüssigkeiten und ihre Beschreibung mit Molekulardynamiksimulationen"
Gerald Mathias
Doktorarbeit, Fakulät für Physik, LMU München

"Angular resolution and range of dipole-dipole correlations in water"
Gerald Mathias and Paul Tavan
J. Chem. Phys. 120, 4393-4403 (2004)

"Continuum description of ionic and dielectric shielding for molecular-dynamics simulations of proteins in solution"
Bernhard Egwolf and Paul Tavan
J. Chem. Phys. 120, 2056-2068 (2004)

"A fast multipole method combined with a reaction field for long-range electrostatics in molecular dynamics simulations: The effects of truncation on the properties of water "
G. Mathias, B. Egwolf, M. Nonella, and P. Tavan
J. Chem. Phys. 118, 10847-10860 (2003)

"Continuum description of solvent dielectrics in molecular-dynamics simulations of proteins"
B. Egwolf and P. Tavan
J. Chem. Phys. 118: 2039-2056 (2003)

"Multiple time step algorithms for molecular dynamics simulations of proteins: How good are they?"
H. Grubmüller, P. Tavan
J. Comput. Chem. 19: 1543-1552, 1998

"FAMUSAMM: A new algorithm for rapid evaluation of electrostatic interactions in molecular dynamics simulations"
M. Eichinger, H. Grubmüller, H. Heller, P. Tavan
J. Comput. Chem. 18: 1729-1749, 1997

"Fast version of the structure adapted multipole method -- Efficient calculation of electrostatic forces in protein dynamics"
C. Niedermeier, P. Tavan
Molecular Simulation 17: 57-66, 1996

"A structure-adapted multipole method for electrostatic interactions in protein dynamics"
C. Niedermeier, P. Tavan
J. Chem. Phys. 101 : 734-748, 1994

"Effiziente Modellierung elektrostatischer Wechselwirkungen in Proteindynamikrechnungen"
Christoph Niedermeier
Doktorarbeit, Institut für Medizinische Optik, Fakultät für Physik, LMU München

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Letzte Änderung: 2024-06-17 19:32