From: Raman Preet Singh (ramanpreetsingh_at_hotmail.com)
Date: Sun Nov 27 2022 - 08:01:01 CST

Hi Angad,

There's a VMD tutorial to measure water permeation through nanotubes. That could be a good starting point. It has a TCL script to study number of water molecules permeating through a CNT. You can modify it to measure ions that remain within a defined distance from DNA over the trajectory frames. I myself am not an expert in TCL so can't be of much help in this regard. However, if you have a script, others on the list can help to address the errors/bugs.

Regards,
Raman

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________________________________
From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of angad sharma <angadsharma54_at_gmail.com>
Sent: Friday, November 25, 2022 12:03:20 PM
To: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: Re: vmd-l_at_ks.uiuc.edu

Dear VMD users,
In my last email regarding the calculation of Residence time of ions around DNA, some of you have suggested the procedure or link to do the same. Thanks a lot to all of them. I am trying but still there are some problems.
Does somebody have a vmd tcl script similar like this(or regarding any kind of residence time calculation ), from where I can figure out my mistakes.
-------------------------------------------------
With Regards
Angad Sharma
Research Scholar
School of Computational & Integrative Sciences
Jawaharlal Nehru University
New Delhi 110067, (INDIA)

On Tue, Nov 22, 2022 at 4:36 PM angad sharma <angadsharma54_at_gmail.com<mailto:angadsharma54_at_gmail.com>> wrote:
Dear VMD users,
In my last email regarding the calculation of Residence time of ions around DNA, some of you have suggested the procedure or link to do the same. Thanks a lot to all of them. I am trying but still there are some problems.
Does somebody have a vmd tcl script similar like this(or regarding any kind of residence time calculation ), from where I can figure out my mistakes.

-------------------------------------------------
With Regards
Angad Sharma
Research Scholar
School of Computational & Integrative Sciences
Jawaharlal Nehru University
New Delhi 110067, (INDIA)