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

[Justin A. Lemkul]

devicerandom wrote:
> On 14/12/10 18:35, Bob Johnson wrote:
>> Can anyone answer this question or guide me somewhere with helpful
>> information?
>> Thanks,
>> Bob
> 
> 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.

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.

-Justin

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================