VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Jul 15 2021 - 09:50:28 CDT

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/

Axel.

On Thu, Jul 15, 2021 at 10:36 AM Fujie Tang <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>
> *Sent:* Thursday, July 15, 2021 1:57 AM
> *To:* Fujie Tang <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
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!v9fNXxTeqcusbfceHjzlc4uusF6s96j3lcfyeGe_rDkZMGwfhNyEK68qWoG4TvdfmQ$ 
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.