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Car–Parrinello Molecular Dynamics Simulations and Biological Systems

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Atomistic Approaches in Modern Biology

Part of the book series: Topics in Current Chemistry ((TOPCURRCHEM,volume 268))

Abstract

The basic concepts of Car–Parrinello molecular dynamics (CPMD) and its application to biological systems are reviewed. In Car–Parrinello simulations the electronic structure is calculated on the fly, i.e., during the course of simulations the potential is adjusted according to the chemical events occurring in the system. This allows for more unbiased simulations of chemical processes, as opposed to classical molecular dynamics, which utilize predefined potentials. In contrast to Born–Oppenheimer molecular dynamics, where the nuclei are propagated under classical equations of motions and where the wave function is calculated in every time step, CPMD maps this two-component classical/quantum system onto a two-component purely classical system. A short introduction into classical mechanics, which provides the equations of motions, is given. DFT will be briefly outlined because it represents the standard method for obtaining the electronic structure during a CPMD simulation. QM/MM approaches, which combine the CPMD method for a core region with a classical description of its environment, are also reviewed. These schemes provide a more reliable description of biological systems, whose properties are strongly influenced by their surroundings. A brief overview over the application of Car–Parrinello simulations to biological systems is provided. Finally, a case study to illustrate some of the basic possibilities of this method is discussed.

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Abbreviations

BOMD:

Born–Oppenheimer molecular dynamics

CPMD:

Car–Parrinello molecular dynamics

DFT:

Density functional theory

GGA:

Generalized gradient approximation

HF:

Hartree–Fock

LDA:

Local density approximation

MD:

Molecular dynamics

MM:

Molecular mechanics

MP2:

Second order Møller–Plesset theory

PP:

Pseudopotential

PW:

Plane wave

QM/MM:

Quantum mechanics/molecular mechanics

TDDFT:

Time-dependent density functional theory

WDA:

Weighted density approximation

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Acknowledgments

We gratefully acknowledge the financial support of the DFG priority program SPP 1191 “Ionic Liquids” and the ERA program, which allows productive collaboration under the project “A Modular Approach to Multi-responsive Surfactant/Peptide (SP) and Surfactant/Peptide/Nanoparticle (SPN) Hybrid Materials”. We would furthermore like to acknowledge the financial support from the collaborative research center SFB 624 “Templates” at the University of Bonn. Fruitful discussion with Jürg Hutter, Ursula Röthlisberger, and Markus Reiher are also gratefully acknowledged. JT would like to thank the Fonds der Chemischen Industrie for a Chemiefonds-Stipendium.

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  1. Institute for Physical and Theoretical Chemistry, Wegelerstr. 12, 53115, Bonn, Germany

    Jens Thar, Werner Reckien & Barbara Kirchner

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  1. Jens Thar
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Correspondence to Barbara Kirchner .

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Markus Reiher

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Thar, J., Reckien, W., Kirchner, B. (2006). Car–Parrinello Molecular Dynamics Simulations and Biological Systems. In: Reiher, M. (eds) Atomistic Approaches in Modern Biology. Topics in Current Chemistry, vol 268. Springer, Berlin, Heidelberg . https://doi.org/10.1007/128_2006_083

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