Journal of Chemical Theory and Computation · 2022 · 11 citations · 93 references
Natural SciencesBiophysicsChemistryComputational BiophysicsStructural BiologyStructural BiophysicsComputational Molecular BiophysicsConformational DynamicsMolecular DynamicsMolecular ModelingMolecular SimulationProtein DynamicsAccelerated Molecular DynamicsFree Energy ChangesMolecular Dynamics Free Energy CalculationsMolecular Dynamics Of ProteinsNonequilibrium DynamicsPotential Of Mean ForceProtein UnfoldingProtein Unfolding Pathways
, with respect to the potential of mean force and hydrogen bonds. We show that the use of telescoping boxes introduces little numerical error while significantly reducing the computational cost.
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VMD: Visual molecular dynamics
William Humphrey, Andrew Dalke, Klaus Schulten · Journal of Molecular Graphics · 1996 · 66.6K citations
Nonequilibrium Equality for Free Energy Differences
Christopher Jarzynski · Physical Review Letters · 1997 · 5.4K citations · Full text