You can manually add 8 Na+ ions if you want. I would suggest that 0.002
charge units from neutrality is better than 0.998. For very small (<0.01)
charges, neutrality is forced by redistributing the extra charge over every
atom (which is a tiny, tiny perturbation). For all other simulations, a
"uniform neutralizing plasma" is assumed, which is a phrase attributed to
the way the reciprocal space is computed in which the term that diverges
for non-zero net charges is assumed to be 0 (which is its value for a
neutral charge, IIRC). However, it's always better to neutralize in these
situations, IMO.
Perhaps people with more knowledge/experience can elaborate on these points.
HTH,
Jason
On Thu, Dec 29, 2011 at 10:41 AM, George Tzotzos <gtzotzos.me.com> wrote:
> Thank you Jason. Probably, the discrepancy comes from my ligand.
>
> One additional question. How critical is inadequate neutralisation, say 7
> instead of 8 Na+?
>
> Regards
>
> George
>
>
> On Dec 29, 2011, at 4:25 PM, Jason Swails wrote:
>
> > On Thu, Dec 29, 2011 at 5:27 AM, George Tzotzos <gtzotzos.me.com> wrote:
> >
> >> This may be a trivial question but any "enlightenment" would be most
> >> welcome.
> >>
> >> tLeap charge COMPLEX gives Total perturbed charge: -7.998000. Yet
> "addions
> >> COMPLEX Na+ 0" produces "7 Na+ ions required to neutralize". Shouldn't
> it
> >> be 8 ions instead?
> >>
> >> Asking this out of curiosity. Thanks in advance for any answer.
> >>
> >
> > The problem is that the charge is cast as an integer (or supplied to the
> > floor() function, I don't know which without looking at the code),
> meaning
> > that any fractional charge is ignored. As close as 0.998 may be to 1, it
> > doesn't actually register as a full charge, and as such is not
> neutralized
> > by addions.
> >
> > It doesn't make much sense to have 0.998 of an electron, so you may check
> > why this charge is coming out this way in the first place. Do you have a
> > custom residue that you derived charges for? If so, I would suggest
> > assigning that 0.002 e-charges somewhere on that residue.
> >
> > HTH,
> > Jason
> >
> >
> >> Regards
> >>
> >> George
> >>
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> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
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> > http://lists.ambermd.org/mailman/listinfo/amber
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>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Dec 29 2011 - 09:00:03 PST
