VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon May 10 2021 - 01:01:05 CDT

Hi,
  FYI, I recently tracked down a memory corruption flaw in AutoPSF which is
almost certainly the cause of the problem reported here.

The flaw had been in the AutoPSF code since it was originally written,
but it started creating the kind of hanging behavior reported here,
and crashing in other cases, particularly with the new revs of MacOS
and certin versions of Ubuntu Linux.

I'm currently tracking down an unrelated but similar type of bug in the
psfgen plugin, and after I've got that resolved, I plan
to post new VMD builds for all platforms.

Best,
  John

On Sun, May 09, 2021 at 08:17:26PM -0400, Peter Freddolino wrote:
> Hi Patrick, Could you please let us know what structure you were trying to
> use autopsf on?
> Thanks,
> Peter
> On Sun, May 9, 2021 at 4:39 PM Patrick Osmer <[1]posmer_at_gmail.com> wrote:
>
> Dear VMD support,
>
> IÂ have recently installed VMD 1.9.4a48-Catalina-Rev7 onto a MacBook Pro
> 16-in running MacOS Catalina 10.15.7. It seemed to be running fine until
> I tried to use the Automatic PSF Builder, which failed to complete the
> â**Iâ**m feeling luckyâ** task and left VMD non-responsive. Is this a
> known problem?
>
> The task has always worked fine for me with VMD 1.9.3, and it also
> worked on a MacBook Air running VMD 1.9.4a51-arm64.Rev9 on macOS Big Sur
> 11.2.3. Iâ**ll appreciate any help or suggestions for fixing the
> problem.
>
> Â
>
> (By the way, pushing the â**full-screenâ** button for the OpenGL Display
> crashes VMD 1.9.4, both on the MacBook Pro and MacBook Air.)
>
> Â
>
> Thanks,
>
> Â
>
> Patrick Osmer
>
> Professor Emeritus
>
> The Ohio State University
>
> [2]osmer.1_at_osu.edu
>
> References
>
> Visible links
> 1. mailto:posmer_at_gmail.com
> 2. mailto:osmer.1_at_osu.edu 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/