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

Mark Abraham Mark.Abraham at anu.edu.au
Fri Nov 18 15:23:51 CET 2011

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 


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