Concept

Energy drift

Publications associées (13)

Biomolecular Simulation: a Perspective from High Performance Computing

Ursula Röthlisberger, Viacheslav Bolnykh, Paolo Carloni

High-Performance Computing is impacting on all biomedical sciences, including molecular biophysics. Here, we describe general parallel computing strategies (multi-threading and distributed computing) used in all the natural sciences, including molecular bi ...

WILEY-V C H VERLAG GMBH2020

Gas-sieving zeolitic membranes fabricated by condensation of precursor nanosheets

Michele Ceriotti, Kumar Varoon Agrawal, Luis Francisco Villalobos Vazquez de la Parra, Mostapha Dakhchoune, Claudia Esther Avalos, Rocio Semino Barbaresi, Yu Han

The synthesis of molecular-sieving zeolitic membranes by the assembly of building blocks, avoiding the hydrothermal treatment, is highly desired to improve reproducibility and scalability. Here we report exfoliation of the sodalite precursor RUB-15 into cr ...

NATURE RESEARCH2020

A combined on-the-fly/interpolation procedure for evaluating energy values needed in molecular simulations

Jiri Vanicek, Konstantin Karandashev

We propose an algorithm for molecular dynamics or Monte Carlo simulations that uses an interpolation procedure to estimate potential energy values from energies and gradients evaluated previously at points of a simplicial mesh. We chose an interpolation pr ...

2019

Anomalous Effects of Velocity Rescaling Algorithms: The Flying Ice Cube Effect Revisited

Berend Smit, Seyedmohamad Moosavi, Efrem Daniel Braun

The flying ice cube effect is a molecular dynamics simulation artifact in which the use of velocity rescaling thermostats sometimes causes violation of the equipartition theorem, affecting both structural and dynamic properties. The reason for this artifac ...

2018

cemff: A force field database for cementitious materials including validations, applications and opportunities

Paul Bowen, Sandra Caroline Galmarini, Aslam Kunhi Mohamed, David Geissbühler

This paper reviews atomistic force field parameterizations for molecular simulations of cementitious minerals, such as tricalcium silicate (C3S), portlandite (CH), tobermorites (model C-S-H). Computational techniques applied to these materials include clas ...

Elsevier2017

Force Field Development from Periodic Density Functional Theory Calculations for Gas Separation Applications Using Metal-Organic Frameworks

Berend Smit, Rocio Mercado, Yongjin Lee, Miguel Gonzalez

We present accurate force fields developed from density functional theory (DFT) calculations with periodic boundary conditions for use in molecular simulations involving M-2(dobdc) (M-MOF-74; dobdc(4-) = 2,5-dioxidobenzenedicarboxylate; M = Mg, Mn, Fe, Co, ...

American Chemical Society2016

Molecular dynamics nano-scratching of aluminium: a novel quantitative energy-based analysis method

Jean-François Molinari, Till Junge

Atomistic models for friction suffer from the severe length- and time-scale restrictions of molecular dynamics. Even when they yield good qualitative results, it is difficult to draw meaningful quantitative conclusions from them. In this paper, a novel app ...

Elsevier Science Bv2012

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA

John Maddocks

It is well recognized that base sequence exerts a significant influence on the properties of DNA and plays a significant role in protein-DNA interactions vital for cellular processes. Understanding and predicting base sequence effects requires an extensive ...

2010

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 ...

2009

Location, Tilt, and Binding: A Molecular Dynamics Study of Voltage-Sensitive Dyes in Biomembranes

Marlon Hinner

We present a molecular dynamics study on the interaction of styryl-type voltage-sensitive dyes with a lipid membrane. In this work, voltage-sensitive dyes are proposed as interesting model amphiphiles for biomolecular simulation, due to the wealth of bioph ...

2009

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