VMD-L Mailing List

From: Daipayan Sarkar (sdaipayan_at_gmail.com)
Date: Thu Nov 10 2022 - 08:02:17 CST

Hi Angad,

You may consider the following steps to do this analysis.

1. After you load the psf and trajectory dcd, wrap the trajectory using PBC tools.
2. Make two VMD atoms selection, one for ion and another for the nucleotide. For the latter selection, you should be careful on what you choose, as I assume selecting all the atoms may not be ideal here.
3. Calculate and save as an array the distances between the ion and DNA molecule, based on atom selections made in the previous step, for your trajectory. Note the distance here is basically a measure of contact and requires the user to make an informed decision on a reasonable choice for a distance-based cutoff for the ions to be in contact with DNA, outside which they are not. Go back to the literature and check what would be a reasonable distance value for this specific purpose.
4. Once the distance array is computed, calculate for how many frames in your trajectory (or reduced trajectory) the user-defined criteria of contact is satisfied. Now, convert the frame index to time, just like how you would when you report length of a simulation. This in my opinion should give you an estimate for the dwell time.

Unfortunately, I don’t have a Tcl version of a Python script that does what I described before, immediately available. But you may consider using the algorithm steps described above to write a Tcl analysis script.

-Daipayan

From: "owner-vmd-l_at_ks.uiuc.edu" <owner-vmd-l_at_ks.uiuc.edu> on behalf of angad sharma <angadsharma54_at_gmail.com>
Date: Thursday, November 10, 2022 at 2:12 AM
To: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: Residence time of ions

Dear VMD users,
Does anyone have an idea how to calculate the residence time of ions around DNA within a fixed cutoff distance ?
Actually I want to calculate the residence time of different ions around DNA. I have no idea how to write a tcl script for this.
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With Regards
Angad Sharma
Research Scholar
School of Computational & Integrative Sciences
Jawaharlal Nehru University
New Delhi 110067, (INDIA)