On Oct 18, 2012, at 4:26 PM, Jason Swails wrote:
> On Thu, Oct 18, 2012 at 2:01 PM, Gustavo Seabra wrote:
>
>> Hi folks,
>>
>> I have yet another question regarding the definition of "intdiel". I
>> understand it is supposedly the dialectric constant "inside" the molecule,
>> as have been discussed previously:
>>
>> http://archive.ambermd.org/201007/0705.html
>> http://archive.ambermd.org/200211/0148.html
>>
>> However, the manual says it a bit differently:
>> "[…] the interior of the atom is assumed to be filled uniformly with a
>> material of dielectric constant 1." (page 47),
>>
>> Then when describing intdiel:
>> "intdiel Sets the interior dielectric constant of the molecule of
>> interest. Default is 1.0. Other values have not been extensively tested."
>> (page 52).
>>
>> My question is about what exactly is set by intdiel. Is it the dielectric
>> in the interior of the ATOM (as within the limits of the atomic radius) or
>> is it the constant in the interior of the MOLECULE (for example, as within
>> a certain radius from the COM of the molecule)?
>>
>
> In GB (like in PB), the environment is roughly partitioned into two
> dielectric regions, the interior of the molecule (solvent inaccessible, low
> internal dielectric) and the exterior of the molecule (solvent accessible,
> high external dielectric).
>
> In GB, the 'effective radius' is basically an average measure of how far
> away a given atom is from the solvent-accessible region (following the Born
> solution of the PB equation to solvating a single charged particle). The
> picture in GB is a little different compared to PB, though.
>
> In PB, the interior dielectric really is the dielectric constant of the
> interior of the protein (sometimes set to ~2 to account for electron
> polarization). In GB, the 'internal' dielectric constant is actually the
> dielectric constant of the medium you're transferring *from*. That is, GB
> measures the free energy of transferring a structure from gas
> (dielectric=1) to solution (dielectric=80), so intdiel actually means
> something different in GB compared to PB. (In the derivation of the GB
> equation, the internal dielectric of the solute actually cancels out)
>
> What people have done is to set the interior dielectric to != 1 in GB and
> said that was equivalent to transferring the solute from a low-dielectric,
> organic solvent with the same dielectric response as the interior of the
> solute, into the high-dielectric, polar solvent.
>
> Hopefully this is clear-ish,
> Jason
Thanks a lot, Jason.
So, from what I gather, the intdiel/extdiel constants in fact have *nothing to do* with the spacial arrangement of the atoms (except from the calculation of the solvent-accessible area), but just define the free energy term of bringing the whole molecule from one medium to another, is that correct?
Gustavo.
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Received on Thu Oct 18 2012 - 16:00:03 PDT
