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Comparison of force-field implementations

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Publications associées (25)

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Carbon Nanotubes : Adsorption, Point Defects and Structural Deformation from Quantum and Classical Simulations

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This thesis studies carbon nanotubes using state-of-the-art computational methods. Using large-scale quantum-mechanical calculations, based on density-functional-theory, we investigate several important aspects of the physics and chemistry of single-walled ...

EPFL2014

Cardiolipin Models for Molecular Simulations of Bacterial and Mitochondrial Membranes

Matteo Dal Peraro, Diane Virginie Marie Lançon, Thomas Lemmin, Christophe Bovigny

Present in bacterial and mitochondrial membranes, cardiolipins have a unique dimeric structure, which carries up to two charges (i.e., one per phosphate group) and, under physiological conditions, can be unprotonated or singly protonated. Exhaustive models ...

Amer Chemical Soc2013

Multiscale simulations of protein dynamics

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Characteristic timescales associated with the function of biomolecules, like proteins, range from femtoseconds up to minutes, whereas their corresponding spatial extent ranges from few ̊A to μm when associating in large macromolecular complexes. Moreover, ...

EPFL2013

Challenges and perspectives in biomolecular simulations: from atomistic picture to multiscale modeling

Matteo Dal Peraro, Michele Cascella

We review the state-of-the-art in computational molecular simulations for biological systems. We limit our discussion to three fields: all-atom simulations, coarse-grained models, and novel multiscale approaches. While molecular dynamics simulations are br ...

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Developing Improved Charge Sets for the Modeling of the KcsA K+ Channel Using QM/MM Electrostatic Potentials

Ursula Röthlisberger, Leonardo Guidoni, Denis Bucher

The performance of popular molecular mechanics (MM) force fields in treating problems that involve ion-channel interactions is explored. We have used quantum mechanical/molecular mechanical (QM/MM) calculations to compute the electrostatic potential inside ...

2009