From: Vermaas, Josh (
Date: Tue Jul 13 2021 - 15:49:35 CDT

What are you measuring the diffusion of, when, and along what axis? If you turn on periodic images for the protein, you’ll find that the ion probably moved outside the box, and then entered into the protein once it had crossed the periodic box edge (possibly multiple times). If you only care about diffusion in z when the ion is within the protein, you can cook up scripts that will calculate diffusion without needing to unwrap the system, but I’m not entirely sure that is what you are trying to measure.


From: <> on behalf of "Ropon-Palacios G." <>
Date: Tuesday, July 13, 2021 at 3:52 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?


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.