431 citations · 934 across the 11 of their papers we have counts for
12 papers
Optimal Intermediate Hamiltonians for Non-Equilibrium Free Energy Calculations: A Numerical Study of Markov Models
David Beyer, Helmut Grubmüller
The Jarzynski relation enables the estimation of equilibrium free energy differences from non-equilibrium, finite-time switching simulations. These estimates usually converge poorl…
The need to implement FAIR principles in biomolecular simulations
Rommie Amaro, Johan Åqvist, Ivet Bahar +125
This letter illustrates the opinion of the molecular dynamics (MD) community on the need to adopt a new FAIR paradigm for the use of molecular simulations. It highlights the necess…
Bayesian electron density determination from sparse and noisy single-molecule X-ray scattering images
Steffen Schultze, Helmut Grubmüller
Single molecule X-ray scattering experiments using free electron lasers hold the potential to resolve both single structures and structural ensembles of biomolecules. However, mole…
Why solvent response contributions to solvation free energies are compatible with Ben-Naim's theorem
Leonard P. Heinz, Helmut Grubmüller
We resolve a seeming paradox arising from a common misinterpretation of Ben-Naim's theorem, which rests on a pairwise decomposition of the Hamiltonian of a molecular solute/solvent…
Small Sample Limit of the Bennett Acceptance Ratio Method and the Variationally Derived Intermediates
Martin Reinhardt, Helmut Grubmüller
Free energy calculations based on atomistic Hamiltonians provide microscopic insight into the thermodynamic driving forces of biophysical or condensed matter systems. Many approach…
GROMACS Implementation of Free Energy Calculations with Non-Pairwise Variationally Derived Intermediates
Martin Reinhardt, Helmut Grubmüller
Gradients in free energies are the driving forces of physical and biochemical systems. To predict free energy differences with high accuracy, Molecular Dynamics (MD) and other meth…
Variationally Derived Intermediates for Correlated Free Energy Estimates between Intermediate States
Martin Reinhardt, Helmut Grubmüller
Free energy difference calculations based on atomistic simulations generally improve in accuracy when sampling from a sequence of intermediate equilibrium thermodynamic states that…
Computing spatially resolved rotational hydration entropies from atomistic simulations
Leonard P. Heinz, Helmut Grubmüller
For a first principles understanding of macromolecular processes, a quantitative understanding of the underlying free energy landscape and in particular its entropy contribution is…
More Bang for Your Buck: Improved use of GPU Nodes for GROMACS 2018
Carsten Kutzner, Szilárd Páll, Martin Fechner +3
We identify hardware that is optimal to produce molecular dynamics trajectories on Linux compute clusters with the GROMACS 2018 simulation package. Therefore, we benchmark the GROM…
Heterogeneous and rate-dependent streptavidin-biotin unbinding revealed by high-speed force spectroscopy and atomistic simulations
Felix Rico, Andreas Russek, Laura Gonzalez +2
Receptor-ligand interactions are essential for biological function and their binding strength is commonly explained in terms of static lock-and-key models based on molecular comple…
Molecular Simulations of the Ribosome and Associated Translation Factors
Lars V. Bock, Michal H. Kolář, Helmut Grubmüller
The ribosome is a macromolecular complex which is responsible for protein synthesis in all living cells according to their transcribed genetic information. Using X-ray crystallogra…
Best bang for your buck: GPU nodes for GROMACS biomolecular simulations
Carsten Kutzner, Szilárd Páll, Martin Fechner +3
The molecular dynamics simulation package GROMACS runs efficiently on a wide variety of hardware from commodity workstations to high performance computing clusters. Hardware featur…