David van der Spoel

发表

Modeling of enzyme–substrate complexes for the metalloproteases MMP-3, ADAM-9 and ADAM-10

Sergio Manzetti, Daniel R. McCulloch, Adrian C. Herington, 2003, J. Comput. Aided Mol. Des..

Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model

Alexander D. MacKerell, Benoît Roux, David van der Spoel, 2015, J. Comput. Chem..

Protein Folding Properties from Molecular Dynamics Simulations

David van der Spoel, Alexandra Patriksson, M. Marvin Seibert, 2006, PARA.

Systematic design of biomolecular force fields

David van der Spoel, 2021 .

Speeding up parallel GROMACS on high‐latency networks

Martin Fechner, Helmut Grubmüller, Carsten Kutzner, 2007, J. Comput. Chem..

Improved GROMACS Scaling on Ethernet Switched Clusters

Martin Fechner, Helmut Grubmüller, Carsten Kutzner, 2006, PVM/MPI.

Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation

Jin Zhang, David van der Spoel, Badamkhatan Tuguldur, 2015, J. Chem. Inf. Model..

MemBuilder: a web-based graphical interface to build heterogeneously mixed membrane bilayers for the GROMACS biomolecular simulation program

Jin Zhang, Seyed Shahriar Arab, David van der Spoel, 2014, Bioinform..

Evaluation of Generalized Born Models for Large Scale Affinity Prediction of Cyclodextrin Host-Guest Complexes

Haiyang Zhang, Hai Yan, David van der Spoel, 2016, J. Chem. Inf. Model..

Virus Capsid Dissolution Studied by Microsecond Molecular Dynamics Simulations

Daniel S. D. Larsson, David van der Spoel, Lars Liljas, 2012, PLoS Comput. Biol..

GROMACS molecule & liquid database

Carl Caleman, David van der Spoel, Paul J. van Maaren, 2012, Bioinform..

Toward a Computational Ecotoxicity Assay

David van der Spoel, Sergio Manzetti, Mickaël G. Delcey, 2020, J. Chem. Inf. Model..

Making Soup: Preparing and Validating Models of the Bacterial Cytoplasm for Molecular Simulation

David van der Spoel, Zahedeh Bashardanesh, Leandro Oliveira Bortot, 2019, J. Chem. Inf. Model..

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

Peter M. Kasson, Jeremy C. Smith, Roland Schulz, 2013, Bioinform..

g_wham—A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates

Bert L. de Groot, Jochen S. Hub, David van der Spoel, 2010 .

Correction to Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation

David van der Spoel, Jin Zhang, Badamkhatan Tuguldur, 2016, J. Chem. Inf. Model..

Ten simple rules on how to create open access and reproducible molecular simulations of biological systems

Arne Elofsson, Anders Wallqvist, Berk Hess, 2019, PLoS Comput. Biol..

An efficient and extensible format, library, and API for binary trajectory data from molecular simulations

Erik Lindahl, Magnus Lundborg, David van der Spoel, 2014, J. Comput. Chem..

Mobility-based prediction of hydration structures of protein surfaces

István Horváth, David van der Spoel, Csaba Hetényi, 2015, Bioinform..

GROMACS: Fast, flexible, and free

Gerrit Groenhof, Berk Hess, Erik Lindahl, 2005, J. Comput. Chem..

Exploration of Interfacial Hydration Networks of Target-Ligand Complexes

István Horváth, David van der Spoel, Csaba Hetényi, 2016, J. Chem. Inf. Model..

Potential impact of an X-ray free electron laser on structural biology

David van der Spoel, Richard Neutze, J. Hajdu, 2004 .

Thermodynamics of hydronium and hydroxide surface solvation.

Carl Caleman, Maarten G. Wolf, Gerrit Groenhof, 2014 .

Towards phase transferable potential functions: Methodology and application to nitrogen

David van der Spoel, Herman J. C. Berendsen, Peter C. Jordan, 1995, The Journal of Chemical Physics.

Brute-force molecular dynamics simulations of Villin headpiece: Comparison with NMR parameters

Erik Lindahl, David van der Spoel, D. Spoel, 2003 .

Space-time evolution of electron cascades in diamond

David van der Spoel, Beata Ziaja, Janos Hajdu, 2002 .

Prediction of N C bond cleavage frequencies in electron capture dissociation of Trp-cage dications by force-field molecular dynamics simulations

Roman A. Zubarev, David van der Spoel, Frank Kjeldsen, 2006 .

Molecular Dynamics Simulations of Water with Novel Shell-Model Potentials

David van der Spoel, D. Spoel, Paul J. van Maaren and, 2001 .

Auger electron cascades in water and ice

Carl Caleman, Nicusor Timneanu, David van der Spoel, 2004 .

The Origin of Layer Structure Artifacts in Simulations of Liquid Water.

David van der Spoel, Paul J. van Maaren, D. Spoel, 2006 .

Prediction of NCα bond cleavage frequencies in electron capture dissociation of Trp-cage dications by force-field molecular dynamics simulations

Roman A. Zubarev, Christopher M. Adams, David van der Spoel, 2006 .

Hawk: the image reconstruction package for coherent X‐ray diffractive imaging

David van der Spoel, Tomas Ekeberg, Filipe R. N. C. Maia, 2010 .

Relationship between electronic properties and drug activity of seven quinoxaline compounds: A DFT study

David van der Spoel, Sergio Manzetti, Payman Roonasi, 2015 .

Probing solution- and gas-phase structures of Trp-cage cations by chiral substitution and spectroscopic techniques

Roman A. Zubarev, Evangelos Papadopoulos, Christopher M. Adams, 2006 .

Detection of Functional Modes in Protein Dynamics

Jochen S. Hub, David van der Spoel, Bert L. de Groot, 2010 .