Thanks so much, Mathias,
Your explanation is really very helpful.
Best regards,
Nadaafiva
Pada tanggal Min, 5 Jul 2020 pukul 01.17 Matias Machado <
mmachado.pasteur.edu.uy> menulis:
> 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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Received on Sat Jul 04 2020 - 12:00:03 PDT
