VMD-L Mailing List

From: Ackad, Edward (eackad_at_siue.edu)
Date: Mon Sep 26 2022 - 14:38:12 CDT

Thank you. Adding the pbc manually fixed the issue.

_________________________________________________________
Edward Ackad, Ph.D<https://urldefense.com/v3/__http://www.siue.edu/*7Eeackad__;JQ!!DZ3fjg!588CefMtYX8l0ljYjmk612fbZghT_gtMX6j7E1lX5lAonV1fuRj1BmmFwR4p-1Ve0P3FH3iJFyG2P7sI7Q$ >
Associate Professor of Physics
Computational Nanophotonics/Biophysics
Southern Illinois University Edwardsville
(618) 650-2390

________________________________
From: Nathan Kern <nathan.kern_at_lehigh.edu>
Sent: Friday, September 23, 2022 3:13 PM
To: Ackad, Edward <eackad_at_siue.edu>
Cc: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Period images not appearing

Are you sure the files you're loading contain PBC info? Alternatively, are you adding the PBC dimensions manually?

Some formats (e.g., .gro, .dcd) contain the box dimensions, but not all do. For those where it's missing, you have to add it manually with pbc<http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/#x1-30003> set<http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/#x1-30003>.

On Fri, Sep 23, 2022 at 4:09 PM Ackad, Edward <eackad_at_siue.edu<mailto:eackad_at_siue.edu>> wrote:
Hi all,
I've been having issues with the periodic images not showing up in vmd 1.9.4a51 and a55 (possibly older versions). It seems like the boxes don't work since no additional image shows up but if I make a lot of images I can see the sending slows by becoming less responsive. I've tried the different render modes and all have the same issues. I've tried turning the rendering off, the representation on/off, drawstyle changes. Nothing changes anything. Moreover, clicking off the Self box does not remove the self image. I've tried loading with psf+pdb and just pdb for many different molecules, it seems to be file independent.

Any ideas?
Thanks!
Eddie

_________________________________________________________
Edward Ackad, Ph.D<https://urldefense.com/v3/__http://www.siue.edu/*7Eeackad__;JQ!!DZ3fjg!--mLijQpVvRhPGx7wR0AvBVWvQtZ3Vfjb_-D9Inr1gSNj5HP58jn7IqpnXt3zxGchn_9f1VHqt_3Y476ZA$>
Associate Professor of Physics
Computational Nanophotonics/Biophysics
Southern Illinois University Edwardsville
(618) 650-2390