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

[Mark Abraham]

On 18/11/2011 8:10 AM, Ben Reynwar wrote:
> 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
> results.
>

I'd be very skeptical unless you can observe many adsorption/desorption 
processes and with explicit solvent (though they're probably mutually 
exclusive).

Mark