Publications associées à GROMACS

High-Throughput Nanopore Fabrication and Classification Using Xe-Ion Irradiation and Automated Pore-Edge Analysis

Aleksandra Radenovic, Andras Kis, Martina Lihter, Mukesh Kumar Tripathi, Mukeshchand Thakur, Sanjin Marion, Michal Daniel Macha

Large-area nanopore drilling is a major bottleneck in state-of-the-art nanoporous 2D membrane fabrication protocols. In addition, high-quality structural and statistical descriptions of as-fabricated porous membranes are key to predicting the corresponding ...

AMER CHEMICAL SOC2022

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

High-throughput computational screening for solid-state Li-ion conductors

Nicola Marzari, Aris Marcolongo, Leonid Kahle

We present a computational screening of experimental structural repositories for fast Li-ion conductors, with the goal of finding new candidate materials for application as solid-state electrolytes in next-generation batteries. We start from similar to 140 ...

ROYAL SOC CHEMISTRY2020

Extreme Scalability of DFT-Based QM/MM MD Simulations Using MiMiC

Ursula Röthlisberger, Simone Meloni, Martin Peter Bircher, Viacheslav Bolnykh, Jógvan Magnus Olsen, Paolo Carloni

We present a highly scalable DFT-based QM/MM implementation developed within MiMiC, a recently introduced multiscale modeling framework that uses a loose-coupling strategy in conjunction with a multiple-program multiple-data (MPMD) approach. The computatio ...

2019

MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry

Ursula Röthlisberger, Simone Meloni, Martin Peter Bircher, Viacheslav Bolnykh, Paolo Carloni

We present a flexible and efficient framework for multiscale modeling in computational chemistry (MiMiC). It is based on a multiple-program multiple-data (MPMD) model with loosely coupled programs. Fast data exchange between programs is achieved through th ...

AMER CHEMICAL SOC2019

Analyzing ion distributions around DNA: sequence-dependence of potassium ion distributions from microsecond molecular dynamics

John Maddocks, Marco Pasi

Microsecond molecular dynamics simulations of B-DNA oligomers carried out in an aqueous environment with a physiological salt concentration enable us to perform a detailed analysis of how potassium ions interact with the double helix. The oligomers studied ...

Oxford University Press2015

Anandamide Hydrolysis in FAAH Reveals a Dual Strategy for Efficient Enzyme-Assisted Amide Bond Cleavage via Nitrogen Inversion

Ursula Röthlisberger, Pablo Campomanes Ramos, Andrea Cavalli, Giulia Palermo

Herein, we combined classical molecular dynamics (MD) and quantum mechanical/molecular mechanics (QM/MM) simulations to unravel the whole catalytic cycle of fatty acid amide hydrolase (FAAH) in complex with anandamide, the main neurotransmitters involved i ...

2015

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

Dissecting the Effects of Concentrated Carbohydrate Solutions on Protein Diffusion, Hydration, and Internal Dynamics

Matteo Dal Peraro, Enrico Spiga, Luciano Andres Abriata, Francesco Piazza

We present herein a thorough description of the effects of high glucose concentrations on the diffusion, hydration and internal dynamics of ubiquitin, as predicted from extensive molecular dynamics simulations on several systems described at fully atomisti ...

Amer Chemical Soc2014

Analyzing ion distributions around DNA

John Maddocks, Marco Pasi

We present a new method for analyzing ion, or molecule, distributions around helical nucleic acids and illustrate the approach by analyzing data derived from molecular dynamics simulations. The analysis is based on the use of curvilinear helicoidal coordin ...

Oxford University Press2014

Reoptimized interaction parameters for the peptide-backbone model compound N-methylacetamide in the GROMOS force field: Influence on the folding properties of two beta-peptides in methanol

Wei Huang, Bruno Araujo Cautiero Horta

Considering N-methylacetamide (NMA) as a model compound, new interaction parameters are developed for the amide function in the GROMOS force field that are compatible with the recently derived 53A6OXY parameter set for oxygen-containing chemical functions. ...

Wiley-Blackwell2012

The effect of loading on surface roughness at the atomistic level

Jean-François Molinari, Guillaume Anciaux, Peter Spijker

One of the key points to better understand the origins of friction is to know how two surfaces in contact adhere to one another. In this paper we present molecular dynamics (MD) simulations of two aluminium bodies in contact, exposed to a range of normal l ...

Springer-Verlag2012