Dear Nada,
Short answer: Yes!!!
Long answer:
SPLIT is valid as long as "No" is greater than the absolute charge value of the solute, so the most simple and practical rule is
if No >= |Q| then use SPLIT !!!
I recognize, I should have written the condition in that way in the thread and in the paper, which is more easy to read/understand.
That was a mistake :-/
Notice that, if No >= 2*|Q| then SPLIT and SLTCAP render almost identical solutions (<1% difference).
In your case No ~ 5*|Q|, which means you are in the very safe region of the SPLIT approximation.
Other important consideration is that the No=Nw*M/56 assumes a water density of 1 g/ml at 25°C, which is reasonably true for all water models I know, and it should be fine along the biological range of temperature (5-60°C). In other cases the conversion factor ("56") may need to be corrected.
A bonus!!! It is possible to add all ions in just one command line ;-)
addionsrand sol Na+ 61 Cl- 50
The benefit of that is you can add a buffer distance between ionic species to avoid initial clusters, if needed...
Best,
Matias
----- Mensaje original -----
De: "Nada Afiva" <nadaafiva.gmail.com>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Viernes, 3 de Julio 2020 16:58:26
Asunto: Re: [AMBER] How to set salt concentration
Dear Clorice and Amber list,
Yes, you are right. So it should be 61 Na+ and 50 Cl- ions.
One thing, as the formula apply when No/Q >=1.
In my case, No/Q= -5.01. Is the formula still apply?
Thanks so much for your helps.
Best regards,
nadaafiva
Pada tanggal Sab, 4 Jul 2020 pukul 02.10 Clorice Reinhardt <
clorice.reinhardt.yale.edu> menulis:
> Hi Nadafiva,
> I think you need to remember to keep the sign in using the equations in the
> forum post. If you only plugged in Q=11, instead of Q=-11, this would
> explain the numbers you obtain.
> All the best,
> Clorice
>
> On Fri, Jul 3, 2020 at 3:01 PM Nada Afiva <nadaafiva.gmail.com> wrote:
>
> > Dear Sir,
> > 50 Na+ and 61 Cl- ions were calculated according to this:
> > http://archive.ambermd.org/202002/0194.html
> >
> > After that would neutralize by adding a number of Na+, so final
> > charge would be zero. Please correct me if I am wrong.
> > Thanks.
> >
> > nadafiva
> >
> > Pada tanggal Jum, 3 Jul 2020 pukul 20.45 David A Case <
> > david.case.rutgers.edu> menulis:
> >
> > > On Fri, Jul 03, 2020, Nada Afiva wrote:
> > >
> > > >I have protein+RNA+ligand with charge -11.00.
> > > >I want salt concentration 0.15 M. Using your formula,
> > > >I have to add 50 Na+ and 61 Cl- ions.
> > >
> > > This seems wrong: you want more cations than anions, in order to
> > > neutralize the negative charge of the solute.
> > >
> > > ....dac
> > >
> > >
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> > >
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> >
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Received on Sat Jul 04 2020 - 11:30:05 PDT
