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

David van der Spoel spoel at xray.bmc.uu.se
Mon Feb 27 09:11:14 CET 2006

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 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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