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

Maxim Fedorov maxim.fedorov at ucd.ie
Sun Feb 26 21:38:02 CET 2006

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.

With kindest regards,


Maxim V. Fedorov
Research Associate.

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