Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models.

By P. Bjelkmar, Per Larsson, M. Cuendet, Berk Hess, Erik Lindahl. Journal of Chemical Theory and Computation, 2010

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Automated Minimization of Steric Clashes in Protein Structures (2011, methodology): “22 In our protocol, we performed an initial conjugate gradient (CG) minimization for 1000 steps, where we considered maximum force less than 200 kJ/mol/nm as criteria for convergence.”
From Proteins to Perturbed Hamiltonians: A Suite of Tutorials for the GROMACS-2018 Molecular Simulation Package [Article v1.0] (2019, methodology): “Examples include the modeling of the σ-hole on halogens in the OPLS3 [69] and CGenFF [83] parameter sets, lone pairs on sulfur atoms in OPLS-AA and OPLS/CM5 [84], in modeling hydrogen-bond acceptors in the Drude polarizable force field [85, 86], and in repartitioning hydrogen masses onto heavier ato”