[gmx-users] Counter ion and PME
lindahl at cbr.su.se
Fri Mar 23 17:26:40 CET 2007
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
On Mar 23, 2007, at 5:14 PM, David Mobley wrote:
>> 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
>> Thanks for your help,
>> Carlo Camilloni
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