I'm not sure what you mean. Do you mean "why bother making the system
neutral?"?
If the above is the question, then it simply relates to the manner in which
simulations of explicit water are performed:
Generally, the system is bounded by some shape that can be repeated in 3
dimensions infinitely (e.g. a rectangular prism or octahedron), in order to
keep the actual explicitly represented system size small and computable,
while also making the interactions of atoms near the boundaries realistic.
If you do this with the system having a net charge, you are suggesting that
your system is part of some giant solution that overall has a massive net
charge, which is clearly unrealistic.
So from the above you can see why if you are doing implicit solvent, or gas
phase simulations, there is no need to try and enforce neutrality. Also
from the above you can see that a real solution (i.e. in the lab, in a
beaker) is net neutral on average for any small volume of it that you want
to examine (otherwise beakers would be flying around the lab at incredible
speeds causing havoc).
~Aron
On Tue, Jan 22, 2013 at 5:41 PM, Mahendra B Thapa <thapamb.mail.uc.edu>wrote:
> Dear AMBER users,
>
> We add ions ( either Na or Cl) to make the
> system neutral; I am interested to know how we can determine the total
> amount of charge of the system( say, protein). For example, in the tutorial
> 1, section 2 , sub-section2.3.1, 18 sodium anions are added to counteract
> the -18 charge of the DNA chain. Similarly, in my system , I have added
> the different number of Na-ions using addions command. What is the theory
> behind it? If possible, please suggest also the relevant papers or other
> materials .
>
> Thanks,
> Mahendra Thapa
> Graduate Student(Physics)
> University of Cincinnati
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Tue Jan 22 2013 - 16:00:02 PST
