VMD-L Mailing List

From: Georcki Ropon (groponp_at_gmail.com)
Date: Tue Aug 24 2021 - 13:05:05 CDT

Thanks so much, for answering, I need 100 mM up and 10 mM down with respect to membrane.

Manually not is best idea.

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________________________________
De: Alec Zander <alec.zander_at_gmail.com>
Enviado: Tuesday, August 24, 2021 1:01:21 PM
Para: Ropon-Palacios G. <groponp_at_gmail.com>
Cc: VMD Mailing List <vmd-l_at_ks.uiuc.edu>
Asunto: Re: vmd-l: Asymmetric concentration gradient

Cool paper! I think your best bet is to write to the authors directly. They seem to have done everything with in house Tcl scripts.

On Mon, Aug 23, 2021, 22:36 Ropon-Palacios G. <groponp_at_gmail.com<mailto:groponp_at_gmail.com>> wrote:

Dear users,

I am trying to simulate a membrane protein system where it has a concentration difference on one side as well as the other, similar to the work of Professor JC Gumbart “Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations”

My question is, how do I ionize or how do I place the ions on both sides with a difference in concentration? Could you please share a script to do this?.

Best,

Geo. 

--
Ropón-Palacios G. BSc., MSc.
Computational biophysicist,
Associate Research,
Laboratorio de Modelagem Computacional,
Departamento de Ciências Exatas,
Universidad Federal de Alfenas, Minas Gerais, Brasil.
Phone: +51 935 055240.
E-mail: groponp_at_gmail.com<mailto:groponp_at_gmail.com>.