Publications related to 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

Dynamic Nuclear Polarization Magic-Angle Spinning Nuclear Magnetic Resonance Combined with Molecular Dynamics Simulations Permits Detection of Order and Disorder in Viral Assemblies

David Lyndon Emsley, Marc Anthony Caporini

We report dynamic nuclear polarization (DNP)-enhanced magic-angle spinning (MAS) NMR spectroscopy in viral capsids from HIV-1 and bacteriophage AP205. Viruses regulate their life cycles and infectivity through modulation of their structures and dynamics. W ...

2019

An Atomistic Look into Bio-inspired Nanoparticles and their Molecular Interactions with Cells

Francesco Stellacci, Alke Fink, Pablo Campomanes Ramos, Stefano Vanni

Nanoparticles (NPs) have sizes that approach those of pathogens and they can interact with the membranes of eukaryotic cells in an analogous fashion. Typically, NPs are taken up by the cell via the plasma membrane by receptor-mediated processes and subsequ ...

SWISS 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, Andrea Cavalli, Pablo Campomanes Ramos, 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

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GROMACS

Microsecond Time-Resolved Cryo-Electron Microscopy

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

Biomolecular Simulation: a Perspective from High Performance Computing

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

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

MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry

Dynamic Nuclear Polarization Magic-Angle Spinning Nuclear Magnetic Resonance Combined with Molecular Dynamics Simulations Permits Detection of Order and Disorder in Viral Assemblies

An Atomistic Look into Bio-inspired Nanoparticles and their Molecular Interactions with Cells

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

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

Graph Chatbot

Chat with Graph Search

Microsecond Time-Resolved Cryo-Electron Microscopy

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

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

MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry

Dynamic Nuclear Polarization Magic-Angle Spinning Nuclear Magnetic Resonance Combined with Molecular Dynamics Simulations Permits Detection of Order and Disorder in Viral Assemblies

An Atomistic Look into Bio-inspired Nanoparticles and their Molecular Interactions with Cells

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

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

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

Biomolecular Simulation: a Perspective from High Performance Computing