Dear Anuja,
If I correctly understand, Na+ is treated classical but it is placed too close to the QM/MM atoms, then just try adding ions randomly (keyword addIonsRand) instead by the electrostatic potential (keywords addIons or addIons2).
As addIonsRand replaces water molecules by ions there is a great chance of placing the ions somewhere else... (by the way it is also a faster method)
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: "emanuele falbo" <falbo.emanuele.gmail.com>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Miércoles, 17 de Julio 2019 13:40:22
Asunto: Re: [AMBER] Adding Na+
Hi,
As David said you just need to make sure that the Na atom isn't in the mask
selection of your qmmm input file.
In order to do it, just check the order of atom indexes in an molecular
editor as VMD, or just with file editor as vim
Cheers
Manuele
Il mer 17 lug 2019, 17:24 Anuja Ware <ware.anuja.p.gmail.com> ha scritto:
> Hello,
> I am doing QM/MM calculations. Before minimisation, I have added four Na+
> ions to neutralize my system using 'addions2 Na+ 0' command. Among them,
> one of Na+ get added into my qm part and I don't want it in the qm
> interactions. So, how can I remove this Na+ and add it to another place in
> order to neutralize the system?
> Please help.
>
> Thank you.
>
>
>
>
>
>
> Anuja.
> _______________________________________________
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> AMBER.ambermd.org
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>
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Received on Wed Jul 17 2019 - 11:00:03 PDT
