431 citations · 871 across the 5 of their papers we have counts for
6 papers
GROMACS in the cloud: A global supercomputer to speed up alchemical drug design
Carsten Kutzner, Christian Kniep, Austin Cherian +4
We assess costs and efficiency of state-of-the-art high performance cloud computing compared to a traditional on-premises compute cluster. Our use case are atomistic simulations ca…
The persistent question of potassium channel permeation mechanisms
Andrei Mironenko, Ulrich Zachariae, Bert L. de Groot +1
Potassium channels play critical roles in many physiological processes, providing a selective permeation route for K+ ions in and out of a cell, by employing a carefully designed s…
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…
Identification of kinetic order parameters for non-equilibrium dynamics
Fabian Paul, Hao Wu, Maximilian Vossel +2
A popular approach to analyze the dynamics of high-dimensional many-body systems, such as macromolecules, is to project the trajectories onto a space of slowly-varying collective v…
Partial least squares for dependent data
Marco Singer, Tatyana Krivobokova, Bert L. de Groot +1
The partial least squares algorithm for dependent data realisations is considered. Consequences of ignoring the dependence for the algorithm performance are studied both theoretica…
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…