[gmx-users] Umbrella Sampling for a single molecule

Sai Pooja saipooja at gmail.com
Tue Jan 25 17:18:03 CET 2011


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?


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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