VMD-L Mailing List

From: Chris Broomell (ccbroomell_at_gmail.com)
Date: Tue Mar 31 2020 - 15:21:49 CDT

Hi John,

Thanks. Here's a basic rundown of the process that I get hung up on.

   - Working files are 5kep and 1dzl
   - I'll load both molecules
   - select "surface" as the drawing method
   - at this point there's a fairly significant lag (expected)
   - when I try to expand the trajectory to all frames (0:59) this is where
   I start getting the error messages. Indeed VMD usually crashes at this
   point.
   - I have a bit more success using MSMS
      - in this case I CAN get an intact surface representation of the
      large VLP but, sometimes, not all of the frames are displayed.

It is absolutely possible that I am "not doing things properly." I don't
know what the best practices are for this kind of workflow.

My endgoal will be to generate representations of the intact VLPs with
various structural elements/sequences highlighted. I'm fine with the
selections/manipulations, etc., but any time I start trying to employ
surface features things get wobbly.

Thanks again for your help.

Chris

On Tue, Mar 31, 2020 at 3:49 PM John Stone <johns_at_ks.uiuc.edu> wrote:

> 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/
>