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

Ben Reynwar ben at reynwar.net
Fri Nov 18 20:42:13 CET 2011

On Fri, Nov 18, 2011 at 7:23 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> 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

I think I asked my question poorly.
In a perfect simulation with explicit solvent and infinite sampling,
roughly what kind of error might one expect for peptide-peptide
interaction energies due to the force field?
Presumably there are papers out there that go into this, but I'm not
finding them.  If anyone knows of any directions to point me in, I'd
really appreciate it.


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