[gmx-users] Re: gb_saltconc in implicit water simulations

[devicerandom]

On 14/12/10 19:04, Justin A. Lemkul wrote:
>> I was going to send a very similar mail -namely, I have a coarse-grain
>> system in vacuum where I'd like to simulate a charged polymer. My idea
>> was that of adding a single "ghost" counter-ion with zero VdW
>> interactions, perhaps keeping it fixed in one corner of the box, but
>> I'd like to know how meaningful it is.
>>
>
> "In vacuum" and "implicit solvent" are very different concepts. If you
> are indeed simulating in a vacuum, I would be willing to bet that your
> charged polymer will rapidly associate with your dummy ion simply due to
> attractive Coulombic interactions that are not screened by any
> intervening solvent.

Heh, I know very well that -and that is one of the reasons I wanted to 
know how does one cope with that.

I mean, if it's a single polymer, perhaps one can naively position 
restrain the ion in a corner of the box, away from the polymer, while 
the polymer stays on its center of mass. But if I want multiple objects 
in my box, I guess it's not going to work.

I'd like very much to use implicit solvent as well but I have to see how 
deep is the performance impact on my model -after all, one does coarse 
grain to be raw but *fast* :)

>
> In regards to the original post, I have seen this question asked and
> ignored several times already, unfortunately. Most of the literature I
> have read (which primarily uses CHARMM) does not specify how counterions
> are handled, if at all. Maybe there is some intrinsic compensating
> factor in CHARMM that I simply don't know about. I found this:
>
> http://dx.doi.org/10.1002/jcc.20874
>
> But again, it uses CHARMM and fancy modified electrostatic models.
>
> I would really hope that someone who knows about the proper GROMACS
> methodology would comment. This has been a curiosity of mine for some
> time, as well. I have not had a pressing need to try out the implicit
> solvent features, but in the absence of being sure of the methodology, I
> am unlikely to do so.

Perhaps the developers of the implicit solvent know about that? I hope so...

m.