VMD-L Mailing List

From: Jason Smith (jason_smith_18_at_sfu.ca)
Date: Tue Aug 24 2021 - 12:11:09 CDT

How many ions do you need to place? If not too many, you could use VMD to manually change some ions/water molecules after doing the standard solvate/ionisation protocol?

Cheers,

-
Jason Smith
Post-Doctoral Fellow
Robert N. Young Lab, Simon Fraser University
8888 University Drive, Burnaby, BC, V5A-1S6
Canada

________________________________
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: Monday, 23 August 2021 7:08:19 PM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: Asymmetric concentration gradient

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>.