B. Hess

发表

Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models.

E. Lindahl, P. Bjelkmar, Per Larsson, 2010, Journal of chemical theory and computation.

Riemann metric approach to optimal sampling of multidimensional free-energy landscapes.

Berk Hess, Viveca Lindahl, Jack Lidmar, 2018, Physical review. E.

Reproducible polypeptide folding and structure prediction using molecular dynamics simulations.

M. Seibert, D. van der Spoel, B. Hess, 2005, Journal of molecular biology.

Determining the shear viscosity of model liquids from molecular dynamics simulations

B. Hess, 2002 .

Orientation restraints in molecular dynamics simulations using time and ensemble averaging.

B. Hess, R. Scheek, 2003, Journal of magnetic resonance.

Hydration thermodynamic properties of amino acid analogues: a systematic comparison of biomolecular force fields and water models.

B. Hess, N. V. D. van der Vegt, 2006, The journal of physical chemistry. B.

Convergence of sampling in protein simulations.

B. Hess, 2002, Physical review. E, Statistical, nonlinear, and soft matter physics.

Improving efficiency of large time‐scale molecular dynamics simulations of hydrogen‐rich systems

Berk Hess, K. Anton Feenstra, Herman J. C. Berendsen, 1999, Journal of computational chemistry.

Analysis and evaluation of channel models: simulations of alamethicin.

Berk Hess, D Peter Tieleman, D. Tieleman, 2002, Biophysical journal.

Stochastic concepts in molecular simulation

B. Hess, 2002 .

Competing adsorption between hydrated peptides and water onto metal surfaces: from electronic to conformational properties.

Berk Hess, Luigi Delle Site, L. Ghiringhelli, 2008, Journal of the American Chemical Society.

Permeability and ammonia selectivity in aquaporin TIP2;1: linking structure to function

B. Hess, M. Andersson, P. Gourdon, 2018, Scientific Reports.

Steady moving contact line of water over a no-slip substrate

S. Zaleski, S. Bagheri, B. Hess, 2020, The European Physical Journal Special Topics.

The Free Energy Barrier for Arginine Gating Charge Translation Is Altered by Mutations in the Voltage Sensor Domain

Christine S. Schwaiger, E. Lindahl, B. Hess, 2012, PloS one.

Flexible constraints : An adiabatic treatment of quantum degrees of freedom, with application to the flexible and polarizable mobile charge densities in harmonic oscillators model for water

Berk Hess, Herman J. C. Berendsen, H. Berendsen, 2002 .

Sampling rare biomolecular events with adaptive pulling simulations

Berk Hess, Viveca Lindahl, Jack Lidmar, 2015 .

Lennard-Jones Lattice Summation in Bilayer Simulations Has Critical Effects on Surface Tension and Lipid Properties.

Berk Hess, Erik Lindahl, Teemu Murtola, 2013, Journal of chemical theory and computation.

On The Importance of Accurate Algorithms for Reliable Molecular Dynamics Simulations

D. van der Spoel, E. Lindahl, B. Hess, 2019 .

Best Practices in Constant pH MD Simulations: Accuracy and Sampling

A. Jansen, B. Hess, P. Buslaev, 2022, Journal of chemical theory and computation.

A comparison of the Spectral Ewald and Smooth Particle Mesh Ewald methods in GROMACS

B. Hess, A. Tornberg, D. S. Shamshirgar, 2017, 1712.04718.

Skin permeability prediction with MD simulation sampling spatial and alchemical reaction coordinates

E. Lindahl, B. Hess, L. Norlén, 2022, Biophysical journal.

Ion pairing in aqueous electrolyte solutions with biologically relevant anions.

B. Hess, N. V. D. van der Vegt, P. Ganguly, 2011, The journal of physical chemistry. B.

GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers

Berk Hess, Teemu Murtola, Szilárd Páll, 2015 .

GROMACS: Fast, flexible, and free

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

LINCS: A linear constraint solver for molecular simulations

Berk Hess, Herman J. C. Berendsen, Henk Bekker, 1997, J. Comput. Chem..

P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation.

Berk Hess, B. Hess, 2008, Journal of chemical theory and computation.

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

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

Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS pdf

Carsten Kutzner, Berk Hess, Erik Lindahl, 2015, EASC.

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation.

Carsten Kutzner, Berk Hess, Erik Lindahl, 2008, Journal of chemical theory and computation.

GROMACS 3.0: a package for molecular simulation and trajectory analysis

Berk Hess, Erik Lindahl, David van der Spoel, 2001 .

A flexible algorithm for calculating pair interactions on SIMD architectures

Berk Hess, Szilárd Páll, B. Hess, 2013, Comput. Phys. Commun..

Cation specific binding with protein surface charges

B. Hess, N. V. D. van der Vegt, 2009, Proceedings of the National Academy of Sciences.

Stability of Hydrophobically Modified Poly(p-phenylenesulfonate) Bundles As Observed by Molecular Dynamics Simulation

B. Hess, M. Sayar, Christian Holm, 2007 .

Photoactivation of the photoactive yellow protein: why photon absorption triggers a trans-to-cis Isomerization of the chromophore in the protein.

Gerrit Groenhof, Berk Hess, Massimo Olivucci, 2004, Journal of the American Chemical Society.

Predictions of Skin Permeability Using Molecular Dynamics Simulation from Two-Dimensional Sampling of Spatial and Alchemical Perturbation Reaction Coordinates

E. Lindahl, B. Hess, L. Norlén, 2022, bioRxiv.

Permeability and ammonia selectivity in aquaporin TIP2;1: linking structure to function

B. Hess, M. Andersson, P. Gourdon, 2018, Scientific Reports.

Long time atomistic polymer trajectories from coarse grained simulations: bisphenol-A polycarbonate.

Kurt Kremer, Berk Hess, Salvador León, 2006, Soft matter.

Heterogeneous Parallelization and Acceleration of Molecular Dynamics Simulations in GROMACS

E. Lindahl, A. Zhmurov, B. Hess, 2020, The Journal of chemical physics.

Further investigation on the validity of Stokes-Einstein behaviour at the molecular level

A. Mark, W. V. Gunsteren, R. Walser, 2001 .

University of Groningen Stochastic concepts in molecular simulation

B. Hess, 2018 .

Scalable Constant pH Molecular Dynamics in GROMACS

A. Jansen, B. Hess, P. Buslaev, 2022, Journal of chemical theory and computation.

Improving Efficiency of Large Time-Scale Molecular Dynamics Simulations of Hydrogen-Rich Systems

Berk Hess, K. Anton Feenstra, Herman J. C. Berendsen, 1999 .

Osmotic coefficients of atomistic NaCl (aq) force fields.

Berk Hess, Christian Holm, B. Hess, 2006, The Journal of chemical physics.

Accelerated weight histogram method for exploring free energy landscapes.

V Lindahl, J Lidmar, B Hess, 2014, The Journal of chemical physics.

Chain packing in polycarbonate glasses.

K. Kremer, B. Hess, J. Schaefer, 2010, The Journal of chemical physics.

Gromacs User Manual Version 4.6

Peter M. Kasson, D. van der Spoel, Gerrit Groenhof, 2013 .

Density functional study of ion hydration for the alkali metal ions (Li+, Na+, K+) and the halide ions (F-, Br-, Cl-).

Berk Hess, Christian Krekeler, Luigi Delle Site, 2006, The Journal of chemical physics.

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..

Asymmetry of wetting and de-wetting on high-friction surfaces originates from the same molecular physics

B. Hess, M. Pellegrino, 2022, Physics of Fluids.

Scaling of the GROMACS 4.6 molecular dynamics code on SuperMUC

Helmut Grubmüller, Carsten Kutzner, Berk Hess, 2014, PARCO.

Direct-Space Corrections Enable Fast Accurate Lorentz-Berthelot Combination Rule Lennard-Jones Lattice Summation

Berk Hess, Erik Lindahl, Christian L. Wennberg, 2015 .

GROMACS—the road ahead

Berk Hess, David van der Spoel, D. van der Spoel, 2011 .

Water–substrate physico-chemistry in wetting dynamics

B. Hess, P. Johansson, A. Carlson, 2015, Journal of Fluid Mechanics.

Nanoscale sheared droplet: volume-of-fluid, phase-field and no-slip molecular dynamics

S. Zaleski, S. Bagheri, B. Hess, 2021, Journal of Fluid Mechanics.

An application of flexible constraints in Monte Carlo simulations of the isobaric--isothermal ensemble of liquid water and ice Ih with the polarizable and flexible mobile charge densities in harmonic oscillators model.

Berk Hess, Herman J C Berendsen, H. Berendsen, 2004, The Journal of chemical physics.

Solvent-averaged potentials for alkali-, earth alkali-, and alkylammonium halide aqueous solutions.

B. Hess, N. V. D. van der Vegt, 2007, The Journal of chemical physics.

Algorithm improvements for molecular dynamics simulations

Berk Hess, Erik Lindahl, Per Larsson, 2011 .

Driving forces for adsorption of amphiphilic peptides to the air-water interface.

Berk Hess, Alessandra Villa, Mehmet Sayar, 2010, The journal of physical chemistry. B.

Probing microscopic material properties inside simulated membranes through spatially resolved three-dimensional local pressure fields and surface tensions.

E. Lindahl, B. Hess, P. Kasson, 2013, Chemistry and physics of lipids.

ScalaLife - Scalable Software Services for Life Sciences

Anne E. Trefethen, Eduard Ayguadé, Erwin Laure, 2012 .

Electrowetting diminishes contact line friction in molecular wetting

B. Hess, P. Johansson, 2019, 1912.09042.

Molecular dynamics study of dislocation nucleation from a crack tip

B. Hess, E. Giessen, B. Thijsse, 2005 .

Modeling multibody effects in ionic solutions with a concentration dependent dielectric permittivity.

Berk Hess, Christian Holm, B. Hess, 2006, Physical review letters.

3₁₀-helix conformation facilitates the transition of a voltage sensor S4 segment toward the down state.

Berk Hess, Erik Lindahl, Pär Bjelkmar, 2011, Biophysical journal.

SHAKE parallelization

R. Elber, B. Hess, A. P. Ruymgaart, 2011, The European physical journal. Special topics.

Similarities between principal components of protein dynamics and random diffusion

B. Hess, Hess, 2000, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

Improving efficiency of large time‐scale molecular dynamics simulations of hydrogen‐rich systems

H. Berendsen, K. Feenstra, B. Hess, 1999, J. Comput. Chem..

Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models.

E. Lindahl, P. Bjelkmar, Per Larsson, 2010, Journal of chemical theory and computation.

On the Path to Optimal Alchemistry

B. Hess, J. Lidmar, M. Lundborg, 2023, The Protein Journal.

Copernicus: A new paradigm for parallel adaptive molecular dynamics

Peter M. Kasson, Vijay S. Pande, Berk Hess, 2011, 2011 International Conference for High Performance Computing, Networking, Storage and Analysis (SC).

Competing adsorption between hydrated peptides and water onto metal surfaces: from electronic to conformational properties.

L. Ghiringhelli, L. Delle Site, B. Hess, 2008, Journal of the American Chemical Society.

Scalable Constant pH Molecular Dynamics in GROMACS

A. Jansen, B. Hess, P. Buslaev, 2022, Journal of Chemical Theory and Computation.

Constant-pH molecular dynamics simulations of progressive activation in a proton-gated ion channel

B. Hess, R. Howard, E. Lindahl, 2024, Biophysical Journal.

GROMEX: A Scalable and Versatile Fast Multipole Method for Biomolecular Simulation

Gerrit Groenhof, Bartosz Kohnke, Thomas R. Ullmann, 2020, Software for Exascale Computing.

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation.

D. van der Spoel, E. Lindahl, B. Hess, 2008, Journal of chemical theory and computation.

Dynamics and structure of Ln(III)-aqua ions: a comparative molecular dynamics study using ab initio based flexible and polarizable model potentials.

B. Hess, A. Villa, H. Saint-Martin, 2009, The journal of physical chemistry. B.