VMD-L Mailing List

From: CHARLES MCCALLUM (cmccallum_at_me.com)
Date: Fri May 06 2022 - 11:25:52 CDT

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 <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
> 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
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ 

--
Mike McCallum
Morada/Stockton CA, USA
cmccallum at me ^dot^ com