VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri May 06 2022 - 11:28:08 CDT

Mike,
  You might watch 'top' in a terminal window and see if your system
is running out of memory. The slowness that began suddenly sounds like
the onset of exhaustion of your machine's physical memory capacity.
You might close any other memory intensive apps while you're running this.

Best,
  John

On Fri, May 06, 2022 at 09:25:52AM -0700, CHARLES MCCALLUM wrote:
> Hi John,
> I have a Colvars SMD simulation that I tested 1379 atoms, 2000 frames
> It loaded the first 25% rather quickly (90 seconds) then started crawling,
> 0.01% a second. This seems familiar to me so maybe it's not a problem as
> long as when it does finish it gives the expected result. It's at 44%
> after 15 minutes. I'm sure if I had certain HBonds selected rather than
> the whole protein it would be faster.
> It is S L O W L Y churning but it is displaying the expected result.
> Best
> Mike
>
> On May 5, 2022, at 10:41 PM, John Stone <[1]johns_at_ks.uiuc.edu> wrote:
> Charles,
> Can you retry the timeline plugin in the VMD 1.9.4a57 build
> that is currently posted on the download page? I'm curious to get
> feedback from people with MacOS X as the new VMD builds use the latest
> Tcl/Tk which is supposed to fix MacOS X issues.
>
> Thanks,
> John Stone
> [2]vmd_at_ks.uiuc.edu
>
> On Tue, Mar 29, 2022 at 05:03:08PM -0700, CHARLES MCCALLUM wrote:
>
> Hello,
> VMD 1.9.4a55 for OS X.
> I know the Timeline plugin has some breaks and there is currently a
> 'timeline-fix.tcl' available the gets at least the Secondary
> Structure
> view working. It may be well-known (at least by the VMD team), but
> the
> H-Bond view is not working. If it's because of the sorry state of
> tcl/tk
> on OS X, I won't worry about it, as I know that's a headache. I
> just want
> to make sure I'm not unique in having the issue. I did not find a
> mention
> of this problem on the VMD-L archive.
> Best
> Mike
> --
> Mike McCallum
> Morada/Stockton CA, USA
> cmccallum at me ^dot^ com
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [3]http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> [4]http://www.ks.uiuc.edu/Research/vmd/
>
> --
> Mike McCallum
> Morada/Stockton CA, USA
> cmccallum at me ^dot^ com
>
> References
>
> Visible links
> 1. mailto:johns_at_ks.uiuc.edu
> 2. mailto:vmd_at_ks.uiuc.edu
> 3. http://www.ks.uiuc.edu/~johns/
> 4. http://www.ks.uiuc.edu/Research/vmd/ 

-- 
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/