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MDAnalysis: A toolkit for the analysis of molecular dynamics simulations.

, , , and . Journal of Computational Chemistry, 32 (10): 2319-2327 (2011)

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Prediction of cyclohexane-water distribution coefficients for the SAMPL5 data set using molecular dynamics simulations with the OPLS-AA force field., , and . Journal of Computer-Aided Molecular Design, 30 (11): 1045-1058 (2016)MDAnalysis: A toolkit for the analysis of molecular dynamics simulations., , , and . Journal of Computational Chemistry, 32 (10): 2319-2327 (2011)Ligandbook: an online repository for small and drug-like molecule force field parameters., , and . Bioinformatics, 33 (11): 1747-1749 (2017)Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways., , , and . PLoS Computational Biology, (2015)Task-parallel Analysis of Molecular Dynamics Trajectories., , , , , , and . CoRR, (2018)Learning Everywhere: Pervasive Machine Learning for Effective High-Performance Computation., , , , , , , , , and 3 other author(s). IPDPS Workshops, page 422-429. IEEE, (2019)Prediction of hydration free energies for aliphatic and aromatic chloro derivatives using molecular dynamics simulations with the OPLS-AA force field., and . Journal of Computer-Aided Molecular Design, 26 (5): 635-645 (2012)SAMPL6: calculation of macroscopic pK a values from ab initio quantum mechanical free energies., , , and . Journal of Computer-Aided Molecular Design, 32 (10): 1203-1216 (2018)Computing ensembles of transitions from stable states: Dynamic importance sampling., , , and . Journal of Computational Chemistry, 32 (2): 196-209 (2011)Parallel Performance of Molecular Dynamics Trajectory Analysis., , , , and . CoRR, (2019)