VMD-L Mailing List

From: Fujie Tang (fujie.tang_at_temple.edu)
Date: Thu Jul 15 2021 - 16:27:57 CDT

Dear Axel,
Thanks for your comment, I solved it by adding -all flag.
Best wishes,
Fujie
________________________________
From: Axel Kohlmeyer <akohlmey_at_gmail.com>
Sent: Thursday, July 15, 2021 10:50 AM
To: Fujie Tang <fujie.tang_at_temple.edu>
Cc: Geist, Norman <norman.geist_at_uni-greifswald.de>; vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: Re: [External] Re: vmd-l: troubles in setting pbc on m1 mac version

That you have troubles using the GUI is not unexpected given your OS and hardware. There have repeatedly been issues with the Tcl/Tk and the FLTK GUI libraries that VMD uses on macOS and that is more true for the latest OS version and if you have different hardware. This is mostly due to the Apple engineers changing things and thus requiring developers of portable software to re-do the porting, which can be particularly difficult for changes in the graphics subsystem. Since VMD is a "consumer" of such libraries, it always takes some time until bugs are fix and updates trickle down to VMD packages. You can easily see that from searching through the VMD mailing list archives.

The pbc set command will only apply the settings to the current frame unless the frame range is set or the -all flag is used. this is the documented behavior:
https://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/9e8708d9479feaa3*7C716e81efb52244738e3110bd02ccf6e5*7C0*7C0*7C637619575178837072*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000&sdata=i5vJ10lZQd8mlL76Q*2FGkOABi7WBoaCPQNt1W2XlWaww*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJQ!!DZ3fjg!pVaMYaSsQTtTbxdTlGyCndMbhKnLlt8qygtcVggC09sEYV5xfJ9OYfRyYDX8jK2R2Q$ >

Axel.

On Thu, Jul 15, 2021 at 10:36 AM Fujie Tang <fujie.tang_at_temple.edu<mailto:fujie.tang_at_temple.edu>> wrote:
Dear Norman,
Thanks for your reply! I found when I use "radial pair distribution function g(r)" module on my M1 macbook, the option "set Unit cell" to input the unit cell in the "Utilities" is not working, I cannot input the info. I cannot change the default values from 0 to others. I tried to TKconsole with the command "pbc set {12.43 12.43 12.43}" it could load the value, the values in the option "set Unit cell" changes to what I set, but when I compute the radial pair distribution function g(r), the error message comes out "measure gofr: unit cell volume is zero" and "There was an error running 'measure gofr': measure gofr: error during g(r) calculation".
Best wishes,
Fujie

________________________________
From: Geist, Norman <norman.geist_at_uni-greifswald.de<mailto:norman.geist_at_uni-greifswald.de>>
Sent: Thursday, July 15, 2021 1:57 AM
To: Fujie Tang <fujie.tang_at_temple.edu<mailto:fujie.tang_at_temple.edu>>
Subject: [External] Re: vmd-l: troubles in setting pbc on m1 mac version

Hey, I think you need to clarify what "not working" means in your case. The plugin is very old and usually works just fine. What problems do you observe? Do you actually have box information loaded?

Bests
Norman Geist

Am Mittwoch, den 14-07-2021 um 19:01 schrieb Fujie Tang:
Dear VMD mailing list subscribers,
Sorry to disturb you, but I am encountering the troubles to set pbc in the verison of version 1.9.4a51 on M1 macbook. The pbc module of the "radial pair distribution function g(r)" is not working. Does anyone know how to solve it?
Thanks in advance!
Best,
Fujie 

---
Dr. Fujie Tang
Postdoctoral Fellow
Department of Physics
Temple University
Philadelphia, PA 19122
Email: fujie.tang_at_temple.edu<mailto:fujie.tang_at_temple.edu>
--
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com<mailto:akohlmey_at_gmail.com>  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!pVaMYaSsQTtTbxdTlGyCndMbhKnLlt8qygtcVggC09sEYV5xfJ9OYfRyYDU_pqnbmA$ <https://urldefense.com/v3/__https://nam10.safelinks.protection.outlook.com/?url=http*3A*2F*2Fgoo.gl*2F1wk0&data=04*7C01*7Cfujie.tang*40temple.edu*7C8ec44d637b0341789e8708d9479feaa3*7C716e81efb52244738e3110bd02ccf6e5*7C0*7C0*7C637619575178847066*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000&sdata=O3gnhTOI6Usa5siJxmfNZGnPdbmnjdl1X9OaBbQxG0M*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSU!!DZ3fjg!pVaMYaSsQTtTbxdTlGyCndMbhKnLlt8qygtcVggC09sEYV5xfJ9OYfRyYDWohylB4A$ >
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.