VMD-L Mailing List

From: CHARLES MCCALLUM (cmccallum_at_me.com)
Date: Fri May 06 2022 - 12:16:06 CDT

Thanks, John.
I will try that.

Best
Mike

> On May 6, 2022, at 9:28 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> 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/ 

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