Hi,
Personally, I rather add ions up to physiological salt concentration,
in addition to counterions, which makes the equilibration quicker,
also accounts for the presence of both positive and negative charges
on the protein surface and, probably mainly due to the latter, has a
stabilizing effect on the proteins in simulation.
Cheers,
Tsjerk
On 3/23/07, Erik Lindahl <[EMAIL PROTECTED]> wrote:
Hi,
Gromacs correctly accounts for both charge and dipole corrections,
but as David says that is just the mathematical part of the problem.
A decade ago it was a pain to equilibrate ions in the system, but
today it's fairly straightforward with an equilibration of 5-10ns. I
can only speak for myself (well, and my students I guess :-), but we
always use neutralizing ions rather than relying on the charge
correction.
Cheers,
Erik
On Mar 23, 2007, at 5:14 PM, David Mobley wrote:
> Carlo,
>
>> I have read in CSC Course Material that it is possible
>> to do not add counter ions in a charged system with
>> PME electrostatics , because gromacs (3.3.1 ?) adds a
>> background uniform charge to neutralize the system.
>> Is this neutralization correct and used in literature?
>
> I can't say much about GROMACS' particular PME implementation here.
> But generally this is what PME is supposed to do for a charged system,
> since it's impossible to do the sum if the system is charged -- it
> introduces a uniform neutralizing background charge.
>
> Is it "correct"? Well, depends on what you mean by correct. Formally,
> the sum works out OK. And since the charge is uniform, it won't affect
> the dynamics/thermodynamics. Of course, in real life there is no such
> thing as a uniform background charge, and neutralization comes from
> counterions. So in that sense it's incorrect.
>
> David Mobley
> UCSF
>
>> Thanks for your help,
>> Carlo Camilloni
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
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