Hi, I am interested in carrying out umbrella sampling for a protein in explicit solvent with the charmm forcefield. I want to impose a harmonic potential in the dihedral space of only some specific atoms in the protein molecule. I am having trouble figuring out a way to apply this using gromacs. Can I get some help on this?
Thanks Pooja p.s. I have seen the tutorial on US by Justin but I am not sure if that is applicable to a single molecule when the purpose is to obtain the free-energy function associated with the transition in dihedral angles of specific some atoms in a protein molecule -- Quaerendo Invenietis-Seek and you shall discover.
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