[gmx-users] non-specific protein-protein interactions

Ben Reynwar ben at reynwar.net
Thu Nov 17 22:10:41 CET 2011

Dear gromacs list,

Does anyone know how well current force fields capture the energetics
of non-specific protein-protein interactions?  I'm simulating a
protein with an arm that alternates between (apparently) non-specific
adsorption to the main-body of the protein and free movement in the
solvent.  Can I place any trust in the results of an MD simulation for
something like this?  I haven't seen any comparison of experimental
results with simulation results of the energetics of non-specific
protein-protein interactions so I'm a little skeptical about it.
Currently I'm using generalized born implicit solvent, which is
perhaps a mistake when solvation energies could be critical to the


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