[gmx-users] Counterions: influence on protein dynamics.

[David van der Spoel]

Maxim Fedorov wrote:
> Dear all,
> 
> I am doing MD simulations of some polypeptide chains. These 
> polypeptides have non-zero net charge; therefore, I should add some 
> counterions into the box to use the PME.
> I am wondering – is there an elegant way to reduce influence of these 
> counterions on polypeptide dynamics?
> Until now I see only two options for that:
> 1)	Constrain ions somewhere far from the solute – but is doesn’t 
> seem a good idea because the solute can move, and, therefore, contact 
> the ions with time.
> 2)	Make a “quasimolecule” - solute +  ions and constrain the bond 
> distances between solute and ions.
> Option 2) was proposed by Anton in some of his respond to the users of 
> the mail-list. It looks better than opt. 1). But … I am a bit worrying 
> about the difference between dynamics of such ‘quasimolecule’ 
> and ‘natural’ dynamics of my polypeptide chain (a hypothetical case 
> without ions).
> Could it help if I equal to zero the ion masses in opt 2)?
> Thank you all in advance.
You just want a big box, many ions and long simulation times. Anything 
else will make referees frown.


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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