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Reoptimized interaction parameters for the peptide-backbone model compound N-methylacetamide in the GROMOS force field: Influence on the folding properties of two beta-peptides in methanol.

B. Horta, Z. Lin, W. Huang, S. Riniker, W. van Gunsteren, and P. Hünenberger. J. Comput. Chem., 33 (24): 1907-1917 (2012)

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Wilfred Hugo van Soldt

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Wilfred Wesemann

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Conformational state-specific free energy differences by one-step perturbation: Protein secondary structure preferences of the GROMOS 43A1 and 53A6 force fields.Z. Lin, W. van Gunsteren, and H. Liu. J. Comput. Chem., 32 (10): 2290-2297 (2011)On the use of multiple-time-step algorithms to save computing effort in molecular dynamics simulations of proteins.M. Pechlaner, C. Oostenbrink, and W. van Gunsteren. J. Comput. Chem., 42 (18): 1263-1282 (2021)Basic ingredients of free energy calculations: A review.C. Christ, A. Mark, and W. van Gunsteren. J. Comput. Chem., 31 (8): 1569-1582 (2010)Estimating relative free energies from a single ensemble: Hydration free energies.H. Schäfer, W. van Gunsteren, and A. Mark. J. Comput. Chem., 20 (15): 1604-1617 (1999)Parametrization of aliphatic CHn united atoms of GROMOS96 force field.X. Daura, A. Mark, and W. van Gunsteren. J. Comput. Chem., 19 (5): 535-547 (1998)Comparison of three enveloping distribution sampling Hamiltonians for the estimation of multiple free energy differences from a single simulation.C. Christ, and W. van Gunsteren. J. Comput. Chem., 30 (11): 1664-1679 (2009)Molecular dynamics simulations of cyclosporin A: The crystal structure and dynamic modelling of a structure in apolar solution based on NMR data.J. Lautz, H. Kessler, R. Kaptein, and W. van Gunsteren. J. Comput. Aided Mol. Des., 1 (3): 219-241 (1987)Practical Aspects of Free-Energy Calculations: A ReviewN. Hansen, and W. van Gunsteren. Journal of Chemical Theory and Computation, 10 (7): 2632-2647 (July 2014)Polarizable coarse-grained models for molecular dynamics simulation of liquid cyclohexane.O. Szklarczyk, E. Arvaniti, and W. van Gunsteren. J. Comput. Chem., 36 (17): 1311-1321 (2015)A GPU solvent-solvent interaction calculation accelerator for biomolecular simulations using the GROMOS software.N. Schmid, M. Bötschi, and W. van Gunsteren. J. Comput. Chem., 31 (8): 1636-1643 (2010)