Dear Nada Afiva,
This question is answered in the following threads:
http://archive.ambermd.org/202002/0194.html
http://archive.ambermd.org/202003/0040.html
I do NOT recommend the strategy of neutralizing then adding salt, this leads to overestimation of the macroscopic salt.
The best way to estimate the volume of the solvent is using the number of water molecules.
Best,
Matias
------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[
http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
[
http://www.sirahff.com]
----- Mensaje original -----
De: "Nada Afiva" <nadaafiva.gmail.com>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Jueves, 2 de Julio 2020 5:34:28
Asunto: Re: [AMBER] How to set salt concentration
Thanks so much for your helps.
I really appreciate it.
Best,
nadaafiva
Pada tanggal Kam, 2 Jul 2020 pukul 11.15 Aashish Bhatt <
aashish.ph16221.inst.ac.in> menulis:
> Dear Nada
>
> Please look at the link
> https://www.phys.ksu.edu/personal/schmit/SLTCAP/SLTCAP.html
>
> Best Regards
>
> Aashish
>
>
> On Thu, Jul 2, 2020 at 9:41 AM Suchetana Gupta <tutulg.gmail.com> wrote:
>
> > You can first set the charge of the system to zero, in Leap by the usual
> > method. And then follow the same commands to add the required number of
> > ions to attain the desired concentration.
> > There is an old thread in this forum regarding this. Please look for it
> for
> > details.
> > Thanks
> > Suchetana
> >
> > On Thu, 2 Jul 2020, 09:25 Nada Afiva, <nadaafiva.gmail.com> wrote:
> >
> > > Dear all,
> > > I would like to simulate receptor-ligand complex and set the salt
> > > concentration 0.1 M.
> > > If anyone knows how to set the concentration, please let me know.
> > > Thank you.
> > >
> > > Nada afiva
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Thu Jul 02 2020 - 06:30:03 PDT
