If the ions are only there to preserve net charge neutrality, then PME has a
'net neutralizing plasma' effect induced by the way the summation is
performed.
Tom Cheatham had a nice post about this a couple years ago:
http://structbio.vanderbilt.edu/archives/amber-archive/2007/4731.php . If
explicit ions are crucial to the system dynamics, then this will obviously
not capture that. However, it does prevent the energies from diverging and
gives reasonable results.
Others' comments/opinions may be forthcoming ;).
Good luck,
Jason
On Fri, Mar 25, 2011 at 2:02 PM, Mahmoud Soliman <mahmoudelkot.gmail.com>wrote:
>
> Dear Amber users
> How serious if I forgot to neutralize the total charge of my system
> (enzyme
> -ligand complex)???
> Best wishes
> Mahmoud
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Mar 25 2011 - 16:00:03 PDT
