Dear Matias and Amber list,
Thanks for the interesting suggestions and reference (I'll read it in
detail soon).
Just wondering if one can generalize this to dividing the charge by n,
where n is the total number of unique ions.
E.g. divide by 3 in case we want a combination of NaCl (2.5 mM) and KCl
(140 mM) at their typical intracellular concentrations.
Using this one can then simulate situations where intracellular Ca ions
increases 10-1000 fold (here we will divide by 5 to account for NaCl, KCl
and CaCl2).
Please let me know your thoughts and if this approach is meaningful.
Thank you.
On Thu, Mar 5, 2020 at 5:55 AM Matias Machado <mmachado.pasteur.edu.uy>
wrote:
> you can also check this previous post:
>
> [http://archive.ambermd.org/202002/0194.html]
>
> Best,
>
> Matias
>
> ----- Mensaje original -----
> De: "Matias Machado" <mmachado.pasteur.edu.uy>
> Para: "AMBER Mailing List" <amber.ambermd.org>
> Enviados: Miércoles, 4 de Marzo 2020 21:23:01
> Asunto: Re: [AMBER] adding Na, K and Cl ions matching intracellular conc
>
> Dear Vaibhav,
>
> I recommend you to use the SPLIT method, which is described here:
>
> Split the Charge Difference in Two! A Rule of Thumb for Adding Proper
> Amounts of Ions in MD Simulations
> [https://doi.org/10.1021/acs.jctc.9b00953]
>
> The keyword "saltcon" has nothing to do in explicit solvent MDs.
>
> Best regards,
>
> Matias Machado
>
> ------------------------------------
> 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: "Vaibhav Dixit" <vaibhavadixit.gmail.com>
> Para: "AMBER Mailing List" <amber.ambermd.org>
> Enviados: Miércoles, 4 de Marzo 2020 9:49:40
> Asunto: [AMBER] adding Na, K and Cl ions matching intracellular conc
>
> Dear All,
> I'm interested in understanding if/which Na, K and Cl ions explicitly enter
> into the active site of a given protein during MD simulation.
> But I can't find a way/trick (from the manual or older posts) to add all
> these ions matching the intracellular concentrations and while keeping the
> system neutral.
> I'm guessing someone in the list must have already done a similar thing.
> Thus can someone please suggest me on this aspect.
> I'm assuming that if this can be done then I'll have to use saltcon=0 to
> avoid GB modelling for salt concentrations.
> Looking forward to receiving valuable suggestions from the list.
>
> Thank you and best regards.
> Vaibhav
>
>
> --
>
> Regards,
>
> Dr. Vaibhav A. Dixit,
>
> Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
> University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
> AND
> Assistant Professor,
> Department of Pharmacy,
> ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> India.
> Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
> http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
> https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
>
> ORCID ID: https://orcid.org/0000-0003-4015-2941
>
> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
>
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--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
P Please consider the environment before printing this e-mail
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Received on Wed Mar 04 2020 - 20:30:02 PST
