VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 31 2020 - 14:46:29 CDT

Hi Chris,
  Which PDB code is running you out of memory? How are you
visualizing it? It should be possible to visualize structures
with say 5 to 10 million atoms even with only 2GB of memory
depending on how it is done. I can give you some advice if you
tell me more about what you're doing.

Best,
  John

On Mon, Mar 30, 2020 at 04:58:00PM -0400, Chris Broomell wrote:
> All,
> One more question:
> Would it be a feasible workaround if I created a subsystem for Linux on my
> Windows machine and ran the 64-bit build for Linux that way (I do have
> 64-bit Win10)? Forgive me if this is an ignorant question...I'm
> ignorant.
> Absent something like this is sounds like I'm sunk until there's a 64-bit
> Windows build available. That being the case...any recommendations for
> working with large pdb files (i'm only doing structural
> visualizations...no dynamics).
> Thanks for your forbearance.
> Chris
> On Mon, Mar 30, 2020 at 3:49 PM <[1]ccbroomell_at_gmail.com> wrote:
>
> Thanks, John, for the response. Enjoy the bunker!
>
> Chris
>
> > On Mar 30, 2020, at 15:01, John Stone <[2]johns_at_ks.uiuc.edu> wrote:
> >
> > Hi guys,
> >Â Catching up on my exploding inbox.
> > Thanks Axel and others, everything said so far here is accurate.
> >
> > I myself have been holding my breath too long for some of the issues
> > on 64-bit APIs to be resolved.
> >
> > The path forward is that I'll make 64-bit VMD builds available, and
> the
> > features that have 64-bit support will be included, and those that
> > don't simply will not.Â
> >
> > I'm looking at workarounds for issues like the proprietary 3-D input
> > device APIs. Some features like the hardware accelerated interactive
> > ray tracing engines on Intel and NVIDIA's hardware only support 64-bit
> > Windows anyway. We'll likely lose a few features, but we'll gain
> others,
> > and the users can choose the best version for the job.
> >
> > I've got a Windows system in my home office / bunker / homeschool
> classroom
> > here during lockdown, so I should be able to work on this despite the
> > current situation with IL state lockdown etc.
> >
> > Best,
> >Â John
> >
> >> On Mon, Mar 30, 2020 at 02:21:25PM -0400, Mortimer Hemmit wrote:
> >> Here's one example:
> >> [3]https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/21572.html
> >>
> >>> On Mon, Mar 30, 2020 at 2:11 PM Axel Kohlmeyer
> <[4]akohlmey_at_gmail.com> wrote:
> >>>
> >>> yes, but don't hold your breath.
> >>> if you search the mailing list archive, you will find multiple
> discussion on the subject and explanations for why there is no 64-bit
> windows version yet.
> >>>
> >>> Axel.
> >>>
> >>> On Mon, Mar 30, 2020 at 1:31 PM <[5]ccbroomell_at_gmail.com> wrote:
> >>>>
> >>>> Thanks for the response. Is there any plan to develop a 64 bit
> windows build?
> >>>>
> >>>> Chris
> >>>>
> >>>> On Mar 30, 2020, at 13:12, Axel Kohlmeyer <[6]akohlmey_at_gmail.com>
> wrote:
> >>>>
> >>>> ???
> >>>> The VMD windows binary is 32bit and thus memory is limited. To use
> more RAM you would need to run on a different OS for which a 64bit
> binary is available.
> >>>>
> >>>> --
> >>>> Dr. Axel Kohlmeyer [7]akohlmey_at_gmail.com [8]http://goo.gl/1wk0
> >>>> College of Science & Technology, Temple University, Philadelphia
> PA, USA
> >>>> International Centre for Theoretical Physics, Trieste, Italy
> >>>>
> >>>> On Mon, Mar 30, 2020, 12:39 Chris Broomell
> <[9]ccbroomell_at_gmail.com> wrote:
> >>>>>
> >>>>> Hi,
> >>>>>
> >>>>> I am comparing structures of larger VLPs and have been running
> into issues when analyzing large files. Typical errors include "failed
> to increase display list memory pool size, system out of memory."Â I'm
> working with surface maps (both the shipped flavor as well as
> MSMS)...mostly cryo and Xray structures of larger VLPs.
> >>>>>
> >>>>> Is it possible to change the amount of memory that is allocated
> for VMD processes?
> >>>>>
> >>>>> If not - are there any recommendations for how to optimize my
> system to mitigate this?
> >>>>>
> >>>>> My system is:
> >>>>> Win10
> >>>>> 16GB RAM
> >>>>> NVIDIA RTX 2070 super (6GB DDR6)
> >>>>>
> >>>>> Thanks in advance for any help that you could offer.
> >>>>>
> >>>>> Chris
> >>>
> >>>
> >>>
> >>> --
> >>> Dr. Axel Kohlmeyer [10]akohlmey_at_gmail.com [11]http://goo.gl/1wk0
> >>> College of Science & Technology, Temple University, Philadelphia PA,
> USA
> >>> International Centre for Theoretical Physics, Trieste. Italy.
> >
> > --
> > NIH Center for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > [12]http://www.ks.uiuc.edu/~johns/Â Â Â Â Â Â Phone: 217-244-3349
> > [13]http://www.ks.uiuc.edu/Research/vmd/Â Â Â
>
> References
>
> Visible links
> 1. mailto:ccbroomell_at_gmail.com
> 2. mailto:johns_at_ks.uiuc.edu
> 3. https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/21572.html
> 4. mailto:akohlmey_at_gmail.com
> 5. mailto:ccbroomell_at_gmail.com
> 6. mailto:akohlmey_at_gmail.com
> 7. mailto:akohlmey_at_gmail.com
> 8. http://goo.gl/1wk0
> 9. mailto:ccbroomell_at_gmail.com
> 10. mailto:akohlmey_at_gmail.com
> 11. http://goo.gl/1wk0
> 12. http://www.ks.uiuc.edu/~johns/
> 13. 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/