Publications related to Comparison of force-field implementations

Roadmap on Machine learning in electronic structure

Michele Ceriotti, Jigyasa Nigam, Andrea Grisafi, Max David Veit

In recent years, we have been witnessing a paradigm shift in computational materials science. In fact, traditional methods, mostly developed in the second half of the XXth century, are being complemented, extended, and sometimes even completely replaced by ...

IOP Publishing Ltd2022

Temperature- and vacancy-concentration-dependence of heat transport in Li3ClO from multi-method numerical simulations

Federico Grasselli

Despite governing heat management in any realistic device, the microscopic mechanisms of heat transport in all-solid-state electrolytes are poorly known: existing calculations, all based on simplistic semi-empirical models, are unreliable for superionic co ...

NATURE PORTFOLIO2022

Gaussian Process Regression for Materials and Molecules

Michele Ceriotti, David Mark Wilkins

We provide an introduction to Gaussian process regression (GPR) machinelearning methods in computational materials science and chemistry. The focus of the present review is on the regression of atomistic properties: in particular, on the construction of in ...

AMER CHEMICAL SOC2021

Molecular simulations of interfacial systems: challenges, applications and future perspectives

Athanasios Nenes, Satoshi Takahama, Mária Lbadaoui-Darvas

We present a comprehensive review of methods and applications of molecular simulations of interfacial systems. We give a detailed overview of the main techniques and major challenges in the following aspects of solid and fluid surfaces: adsorption at solid ...

TAYLOR & FRANCIS LTD2023

Incompleteness of Atomic Structure Representations

Michele Ceriotti, Sergey Pozdnyakov, Michael John Willatt

Many-body descriptors are widely used to represent atomic environments in the construction of machine-learned interatomic potentials and more broadly for fitting, classification, and embedding tasks on atomic structures. There is a widespread belief in the ...

AMER PHYSICAL SOC2020

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

Accuracy of Molecular Simulation-Based Predictions of k(off) Values: A Metadynamics Study

Ursula Röthlisberger, Simone Meloni, Viacheslav Bolnykh, Michele Parrinello, Paolo Carloni

The k(off) values of ligands unbinding to proteins are key parameters for drug discovery. Their predictions based on molecular simulation may under- or overestimate experiment in a system- and/or technique-dependent way. Here we use an established method-i ...

AMER CHEMICAL SOC2020

Accelerating materials discovery for solid state electrolytes

Matthieu Gilles Mottet

The development of new solid-state electrolytes is a key step in improving the performance and safety of battery technology. Although the use of first-principle methods has proved invaluable in better understanding the process at play in these materials, ...

EPFL2020

The Role of Post-translational Modifications on the Energy Landscape of Huntingtin N-Terminus

Hilal Lashuel, Charlotte Julie Caroline Gehin

Huntington disease is a neurodegenerative disease characterized by a polymorphic tract of polyglutamine repeats in exon 1 of the huntingtin protein, which is thought to be responsible for protein aggregation and neuronal death. The polyglutamine tract is p ...

2019

Water Activity from Equilibrium Molecular Dynamics Simulations and Kirkwood-Buff Theory

Satoshi Takahama, Mária Lbadaoui-Darvas

Water activity and related thermodynamic properties are calculated for several aqueous solutions using equilibrium molecular dynamics in conjunction with the recent extension of the Kirkwood-Buff (KB) theory for closed systems. The general applicability of ...

AMER CHEMICAL SOC2019

AMBER and CHARMM Force Fields Inconsistently Portray the Microscopic Details of Phosphorylation

Veronika Juraskova

Phosphorylation of serine, threonine, and tyrosine is one of the most frequently occurring and crucial post-translational modifications of proteins often associated with important structural and functional changes. We investigated the direct effect of phos ...

AMER CHEMICAL SOC2019

Ab Initio Flexible Force Field for Metal-Organic Frameworks Using Dummy Model Coordination Bonds

Berend Smit, Seyedmohamad Moosavi, Matthew David Witman, Sudabeh Jawahery, Nakul Rampal

We present force fields developed from periodic density functional theory (DFT) calculations that can be used in classical molecular simulations to model M MOF-74 (M = Co, Fe, Mg, Mn, Ni, Zn) and its extended linker analogs. Our force fields are based on c ...

2019

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 ...

Pergamon-Elsevier Science Ltd2017

Classical Force Fields Tailored for QM Applications: Is It Really a Feasible Strategy?

Oliviero Andreussi

Classical molecular dynamics is more and more often coupled to quantum mechanical based techniques as a statistical tool to sample configurations of molecular systems embedded in complex environments. Nonetheless, the classical potentials describing the mo ...

Amer Chemical Soc2017

Mapping the conformational free energy of aspartic acid in the gas phase and in aqueous solution

Michele Ceriotti, Kevin Rossi

The conformational free energy landscape of aspartic acid, a proteogenic amino acid involved in a wide variety of biological functions, was investigated as an example of the complexity that multiple rotatable bonds produce even in relatively simple molecul ...

American Institute of Physics2017

Origin of the Strong Interaction between Polar Molecules and Copper(II) Paddle-Wheels in Metal Organic Frameworks

Berend Smit, Daniele Ongari, Davide Tiana

The copper paddle-wheel is the building unit of many metal organic frameworks. Because of the ability of the copper cations to attract polar molecules, copper paddle-wheels are promising for carbon dioxide adsorption and separation. They have therefore bee ...

American Chemical Society2017

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

Accuracy of Protein Embedding Potentials: An Analysis in Terms of Electrostatic Potentials

Quantum-mechanical embedding methods have in recent years gained significant interest and may now be applied to predict a wide range of molecular properties calculated at different levels of theory. To reach a high level of accuracy in embedding methods, b ...

Amer Chemical Soc2015

Ab Initio Derived Force Fields for Predicting CO2 Adsorption and Accessibility of Metal Sites in the Metal-Organic Frameworks M-MOF-74 (M = Mn, Co, Ni, Cu)

Wendy Lee Queen, Peng Bai

Metal-organic frameworks (MOFs) are versatile nanoporous materials that have gained significant interest as low heat capacity, high selectivity sorbents for CO2 capture applications. Large-scale atomistic simulations for identifying high-performance MOFs a ...

Amer Chemical Soc2015

Generalized QM/MM Force Matching Approach Applied to the 11-cis Protonated Schiff Base Chromophore of Rhodopsin

Ursula Röthlisberger, Ivano Tavernelli, Pablo Campomanes Ramos, Manuel Dömer

We extended a previously developed force matching approach to systems with covalent QM/MM boundaries and describe its user-friendly implementation in the publicly available software package CPMD. We applied this approach to the challenging case of the reti ...

2014