From: Raman Preet Singh (ramanpreetsingh_at_hotmail.com)
Date: Mon Aug 19 2024 - 03:38:33 CDT

Hello Josh,

Thank you for your reply. The equation of sphere did work great to select the atoms on surface.

Regards,
Raman


________________________________
From: Vermaas, Josh <vermaasj_at_msu.edu>
Sent: Friday, August 16, 2024 9:41 PM
To: Raman Preet Singh <ramanpreetsingh_at_hotmail.com>; vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Select atoms on surface of sphere


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