AG Tavan - Projects

LMU München
Fakultät für Physik




(c) 2002 BMO

Polarizable force fields for molecular mechanics from first principles
(Protein dynamics in their native environment)

Molecular mechanical (MM) force fields treat atoms as point masses. Forces are derived from semi-empirical potentials that approximate the chemical and electrostatic interactions. Parameters for the potentials are usually derived from quantum mechanical calculations and experiments at various molecular configurations.

Classical force fields like i.e. CHARMM [1] use fixed partial charges to describe the Coulomb interactions between molecules and distant parts of large molecules. The choice of values for these charges mimics polarization effects within the average electric field exerted by the environment on a given molecule. For isotropic and homogeneous fluids this mean field approximation may be adequate. However, for amino acids in proteins a fixed parameter set cannot account for the specific and diverse electric environments experienced by these building blocks.

Despite the impressive progress in molecular dynamics methods, which calculate forces quantum mechanically (QM) during simulations [2], applications to long-time dynamics of large molecular systems remain computationally unfeasable.

In this project, classical force fields including the molecular polarizability are calculated using QM density functional theory and QM/MM hybrid methods.

[1] "CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations"
Bernard R. Brooks, Robert E. Bruccoleri, Barry D. Olafson, David J. States, S. Swaminathan, and Martin Karplus,
J. Comp. Chem., 4(2):187-217, 1983.

[2] "Structural, electronic, and bonding properties of liquid water from first principles"
P. L. Silvestrelli and M. Parrinello, J. Chem. Phys., 111:3572-3580, 1999.

Previous coworkers:  Philipp Troester
Christoph Wichmann
Andreas Weiss
Magnus Schwörer
Verena Schultheis
Bernhard Schropp
Benjamin Rieff
Gerald Mathias
Paul Tavan

Publications:  "A polarizable QM/MM approach to the molecular dynamics of amide groups solvated in water"
Magnus Schwörer, Christoph Wichmann, and Paul Tavan
J. Chem. Phys. 144, 114504 (2016).

"Simulated Solute Tempering in Fully Polarizable Hybrid QM/MM Molecular Dynamics Simulations"
Magnus Schwörer, Christoph Wichmann, Erik Gawehn, Gerald Mathias
J. Chem. Theory Comput. 12, 992−999 (2016).

"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).

"Polarizable Six-Point Water Models from Computational and Empirical Optimization"
Philipp Tröster, Konstantin Lorenzen, and Paul Tavan
J. Phys. Chem. B 118, 1589-1602 (2014).

"The Microscopic Physical Cause for the Density Maximum of Liquid Water"
Philipp Tröster and Paul Tavan
J. Phys. Chem. Lett. 5, 138−142 (2014).

"Polarizable water models from mixed computational and empirical optimization"
Philipp Tröster, Konstantin Lorenzen, Magnus Schwörer, Paul Tavan
J. Phys. Chem. B 117, 9486−9500 (2013).

"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).

"Spectroscopic polarizable force field for amide groups in polypeptides"
Bernhard Schropp, Christoph Wichmann, and Paul Tavan
J. Phys. Chem. B 114, 6740-6750 (2010).

"Flexibility does not change the polarizability of water molecules in the liquid"
Bernhard Schropp and Paul Tavan
J. Phys. Chem. B 114, 2051-2057 (2010)

"The polarizability of point-polarizable water models: DFT/MM results"
Bernhard Schropp and Paul Tavan
J. Phys. Chem. B 112, 6233-6240 (2008)

"Erweiterung und Anwendung der strukturadaptierten Multipolmethode für polarisierbare Kraftfelder am Beispiel reinen Wassers"
Rieff Benjamin
Dipolmarbeit am Lehrstuhl für Biomolekulare Optik (LMU)

"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.

"Entwicklung von polarisierbaren Wassermodellen für Molekulardynamiksimulationen"
A. Weiss
Diplomarbeit, Lehrstuhl für BioMolekulare Optik, Fakultät für Physik, LMU München, Juli 2001

"A hybrid method for solutes in complex solvents: Density functional theory combined with empirical force fields"
M. Eichinger, P. Tavan, J. Hutter und M. Parrinello
J. Chem. Phys. 110: 10452-10467 (1999)

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Letzte Änderung: 2016-08-31 08:07