Bert L. de Groot

According to our database, Bert L. de Groot authored at least 24 papers between 1997 and 2025.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of five.

2025

Scaling of the GROMACS Molecular Dynamics Code to 65k CPU Cores on an HPC Cluster.

Carsten Kutzner, Vedran Miletic, Karen Palacio Rodríguez, Markus Rampp, Gerhard Hummer, Bert L. de Groot, Helmut Grubmüller

J. Comput. Chem., 2025

2024

Resolving coupled pH titrations using alchemical free energy calculations.

Carter J. Wilson, Bert L. de Groot, Vytautas Gapsys

J. Comput. Chem., June, 2024

Current State of Open Source Force Fields in Protein-Ligand Binding Affinity Predictions.

David F. Hahn, Vytautas Gapsys, Bert L. de Groot, David L. Mobley, Gary Tresadern

J. Chem. Inf. Model., 2024

2022

GROMACS in the Cloud: A Global Supercomputer to Speed Up Alchemical Drug Design.

Carsten Kutzner, Christian Kniep, Austin Cherian, Ludvig Nordstrom, Helmut Grubmüller, Bert L. de Groot, Vytautas Gapsys

J. Chem. Inf. Model., 2022

Pre-Exascale Computing of Protein-Ligand Binding Free Energies with Open Source Software for Drug Design.

Vytautas Gapsys, David F. Hahn, Gary Tresadern, David L. Mobley, Markus Rampp, Bert L. de Groot

J. Chem. Inf. Model., 2022

2021

Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software.

Yuriy Khalak, Gary Tresadern, Bert L. de Groot, Vytautas Gapsys

J. Comput. Aided Mol. Des., 2021

2020

The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations.

Andrea Rizzi, Travis Jensen, David R. Slochower, Matteo Aldeghi, Vytautas Gapsys, Dimitris Ntekoumes, Stefano Bosisio, Michail Papadourakis, Niel M. Henriksen, Bert L. de Groot, Zoe Cournia, Alex Dickson, Julien Michel, Michael K. Gilson, Michael R. Shirts, David L. Mobley, John D. Chodera

J. Comput. Aided Mol. Des., 2020

2019

More bang for your buck: Improved use of GPU nodes for GROMACS 2018.

Carsten Kutzner, Szilárd Páll, Martin Fechner, Ansgar Esztermann, Bert L. de Groot, Helmut Grubmüller

J. Comput. Chem., 2019

Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset.

Eddy Elisée, Vytautas Gapsys, Nawel Mele, Ludovic Chaput, Edithe Selwa, Bert L. de Groot, Bogdan I. Iorga

J. Comput. Aided Mol. Des., 2019

2017

pmx Webserver: A User Friendly Interface for Alchemistry.

Vytautas Gapsys, Bert L. de Groot

J. Chem. Inf. Model., 2017

2015

Best bang for your buck: GPU nodes for GROMACS biomolecular simulations.

Carsten Kutzner, Szilárd Páll, Martin Fechner, Ansgar Esztermann, Bert L. de Groot, Helmut Grubmüller

J. Comput. Chem., 2015

pmx: Automated protein structure and topology generation for alchemical perturbations.

Vytautas Gapsys, Servaas Michielssens, Daniel Seeliger, Bert L. de Groot

J. Comput. Chem., 2015

2013

Collective Dynamics Underlying Allosteric Transitions in Hemoglobin.

Martin D. Vesper, Bert L. de Groot

PLoS Comput. Biol., 2013

Probing the Energy Landscape of Activation Gating of the Bacterial Potassium Channel KcsA.

Tobias Linder, Bert L. de Groot, Anna Stary-Weinzinger

PLoS Comput. Biol., 2013

Computational analysis of local membrane properties.

Vytautas Gapsys, Bert L. de Groot, Rodolfo Briones

J. Comput. Aided Mol. Des., 2013

2012

Ubiquitin Dynamics in Complexes Reveal Molecular Recognition Mechanisms Beyond Induced Fit and Conformational Selection.

Jan H. Peters, Bert L. de Groot

PLoS Comput. Biol., 2012

2010

Conformational Transitions upon Ligand Binding: Holo-Structure Prediction from Apo Conformations.

Daniel Seeliger, Bert L. de Groot

PLoS Comput. Biol., 2010

Spontaneous Quaternary and Tertiary T-R Transitions of Human Hemoglobin in Molecular Dynamics Simulation.

Jochen S. Hub, Marcus B. Kubitzki, Bert L. de Groot

PLoS Comput. Biol., 2010

Ligand docking and binding site analysis with PyMOL and Autodock/Vina.

Daniel Seeliger, Bert L. de Groot

J. Comput. Aided Mol. Des., 2010

2009

Detection of Functional Modes in Protein Dynamics.

Jochen S. Hub, Bert L. de Groot

PLoS Comput. Biol., 2009

tCONCOORD-GUI: Visually supported conformational sampling of bioactive molecules.

Daniel Seeliger, Bert L. de Groot

J. Comput. Chem., 2009

2007

Speeding up parallel GROMACS on high-latency networks.

Carsten Kutzner, David van der Spoel, Martin Fechner, Erik Lindahl, Udo W. Schmitt, Bert L. de Groot, Helmut Grubmüller

J. Comput. Chem., 2007

2006

Improved GROMACS Scaling on Ethernet Switched Clusters.

Carsten Kutzner, David van der Spoel, Martin Fechner, Erik Lindahl, Udo W. Schmitt, Bert L. de Groot, Helmut Grubmüller

Proceedings of the Recent Advances in Parallel Virtual Machine and Message Passing Interface, 2006

1997

A comparison of techniques for calculating protein essential dynamics.

Daan M. F. van Aalten, Bert L. de Groot, John B. C. Findlay, Herman J. C. Berendsen, Andrea Amadei

J. Comput. Chem., 1997