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The cause to use restrains is due to a previous knowledge (i.e. experimental) of system behavior/characteristics that you want to include/retain/reproduce in your simulations. In the case of protein-ligand complex simulations, they encode specifically prior knowledge about the macromolecular system to be simulated and is built of several components. These ...


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I'd use OpenMM's openmmforcefields package, which is available on GitHub. I haven't used it extensively, but I recommended to a student in a colleague's lab and they've found it useful. Small molecule force fields: GAFF 1.x and 2.x parameters OpenFF parameters Biomolecule force fields: Amber-type (albeit not Amber ff19SB yet) CHARMM-type And it will, if ...


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