VMD-L Mailing List

From: Ropon-Palacios G. (groponp_at_gmail.com)
Date: Tue Jul 13 2021 - 14:01:04 CDT

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.