[gmx-users] Counterions: influence on protein dynamics.
maxim.fedorov at ucd.ie
Sun Feb 26 21:38:02 CET 2006
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
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
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