From: Ropon-Palacios G. (groponp_at_gmail.com)
Date: Tue Jul 13 2021 - 15:36:43 CDT

Dear Eric,

 

When the ions are wrapped, I can see how they enter the pore, but when I unwrap ions, at no time do they enter the pore, that was my doubt, because when unwrapped, I no longer observed the phenomenon. Is this physically real, or am I observing something not real when wrapping the ions?

 

--
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. 
 
 
 
 
 
From: Eric Schibli <eric_schibli_at_sfu.ca>
Date: Tuesday, July 13, 2021 at 3:31 PM
To: "Ropon-Palacios G." <groponp_at_gmail.com>, vmd-L <vmd-l_at_ks.uiuc.edu>
Subject: Re: Unwrap for diffusion phenomena? 
 
Hello Ropón-Palacios,
 
Unwrapping ensures that the ions are not wrapped around the periodic boundary. It is necessary to unwrap before calculating displacements or self-diffusion coefficients to eliminate the nonphysical large jumps in position that come with wrapping, but if you are interested in viewing the ions' path relative to your protein, you can keep them wrapped,
 
Eric M. Schibli, PhD
Research Assossiate
Frisken Lab, Simon Fraser University
From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Ropon-Palacios G. <groponp_at_gmail.com>
Sent: Tuesday, July 13, 2021 12:01:04 PM
To: vmd-L
Subject: vmd-l: Unwrap for diffusion phenomena? 
 
Dear users,
 
I have a perhaps trivial question. I have a protein that transposes ions, when I keep the ions wrap I see that they tend to be transported (they enter the ion channel), and when I unwrap the ions (pbc unwrap -sel "ions" -all) I don't see any ion even close to the protein within a radius of 4 Angstroms. I have read that to evaluate diffusion the system has to be unwrap, it is correct, what are you doing?
 
Greetings,
 
--
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.