VMD-L Mailing List

From: Vermaas, Josh (vermaasj_at_msu.edu)
Date: Fri Aug 16 2024 - 11:11:34 CDT

While you can’t do ^2, since I think the parser can’t understand what ^ does, you can do the following:


set patchsel [atomselect top "(x*x)+(y*y)+(z*z)>85"]

This is what I used when I needed to find the surface atoms on a nanoparticle.

-Josh

From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of Raman Preet Singh <ramanpreetsingh_at_hotmail.com>
Date: Friday, August 16, 2024 at 11:17 AM
To: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: Select atoms on surface of sphere

Hi All,

I have created a coordinates file of a spherical nanoparticle and want to modify the surface groups. For this, I need the index of atoms on surface. I tried using the surface command as: surface top 1 2.5 2.5. However, the Tk console gave an error message: invalid command name "surface".

Another approach I tried was
set sel [atomselect top all]
surface $sel 1 2.5 2.5
This also gave the error message: invalid command name "surface"

I also tried selecting atoms using equation of sphere (x^2 + y^2 + z ^2 > r^2) but this too was
An alternative method I could think of is to identify atoms within a certain cutoff from solvent. Since the topology of nanoparticle is not yet ready, the equilibration steps with solvent could not be performed thus I dropped this approach.

Can anyone please guide through this.

Thanks,
Raman