92 citations · 160 across the 4 of their papers we have counts for
4 papers
Software package for simulations using the coarse-grained CALVADOS model
Sören von Bülow, Ikki Yasuda, Fan Cao +6
We present the CALVADOS package for performing simulations of biomolecules using OpenMM and the coarse-grained CALVADOS model. The package makes it easy to run simulations using th…
Machine learning methods to study sequence-ensemble-function relationships in disordered proteins
Sören von Bülow, Giulio Tesei, Kresten Lindorff-Larsen
Recent years have seen tremendous developments in the use of machine learning models to link amino acid sequence, structure and function of folded proteins. These methods are, howe…
Systematic errors in diffusion coefficients from long-time molecular dynamics simulations at constant pressure
Sören von Bülow, Jakob Tómas Bullerjahn, Gerhard Hummer
In molecular dynamics simulations under periodic boundary conditions, particle positions are typically wrapped into a reference box. For diffusion coefficient calculations using th…
Optimal estimates of diffusion coefficients from molecular dynamics simulations
Jakob Tómas Bullerjahn, Sören von Bülow, Gerhard Hummer
Translational diffusion coefficients are routinely estimated from molecular dynamics simulations. Linear fits to mean squared displacement (MSD) curves have become the de facto sta…