VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jul 10 2019 - 15:54:03 CDT

Hi Wasim,
  I just made fresh VMD builds and an updated Linux binary
with the 256-bond-per-atom max bond count. The errors you encountered in the
previous build were completely unrelated to the max bond count change
and have been cured in the new test build. If you're using an older
NVIDIA driver (or no NVIDIA GPU) you'll still get that OptiX startup
error, but you can ignore that. I've posted the new 256-bond-per-atom
build for you here:
  http://www.ks.uiuc.edu/Research/vmd/alpha/256bonds/vmd-1.9.4a35.bin.LINUXAMD64.opengl.tar.gz

Please try it out and let me know if you still have difficulties.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jul 03, 2019 at 11:39:12AM +0530, Wasim Abdul wrote:
> Hi John,
> These errors are appearing when I try to start vmd:
> OptiXRenderer) ERROR: Failed to load the OptiX shared library.
> OptiXRenderer) Â Â Â Â NVIDIA driver may be too old.
> OptiXRenderer) Â Â Â Â Check/update NVIDIA driver
> The autopsf package could not be loaded:
> The mdff_gui package could not be loaded:
> The molefacture package could not be loaded:
> The qwikmd package could not be loaded:
> It is not showing the structure of my polymer too.
> On Sat, Jun 29, 2019 at 12:17 AM Wasim Abdul
> <[1]wasimorbrooklyn2013_at_gmail.com> wrote:
>
> Thank you so so much. I'll try it and let you know.Â
> On Fri 28 Jun, 2019, 9:50 PM John Stone, <[2]johns_at_ks.uiuc.edu> wrote:
>
> Hi Wasim,
> Â I've posted a 256-bond-per-atom test build for you here.Â
> Please try it, and let me know if that resolves your max bond count
> problem or not:
> Â
> [3]http://www.ks.uiuc.edu/Research/vmd/alpha/256bonds/vmd-1.9.4a34.bin.LINUXAMD64.opengl.tar.gz
>
> It may be possible to eliminate the compile-time limited maximum bond
> count
> in the future, but I'll have to look closely at the practicality and
> invasiveness of the required changes and their performance cost to
> determine
> whether I'm willing to do the necessary rearchitecture in VMD.
>
> Best,
> Â John Stone
> Â [4]vmd_at_ks.uiuc.edu
>
> On Fri, Jun 28, 2019 at 12:12:49PM +0530, Wasim Abdul wrote:
> >Â Â Hi John,
> >Â Â I have a maximum of 221 bonds for one of the beads of the
> polymer. Can a
> >Â Â maximum limit of 250 be set? I'm usingÄ*
> >Â Â carbon as the atom for a bead of the polymer.
> >Â Â Thank you.
> >Â Â On Thu, Jun 27, 2019 at 7:40 PM Wasim Abdul
> >Â Â <[1][5]wasimorbrooklyn2013_at_gmail.com> wrote:
> >
> >Â Â Â I'm using Linux. I'll count the maximum number of bonds I
> have and
> >Â Â Â letÄ* you know. Thank you so so much.
> >Â Â Â On Thu 27 Jun, 2019, 7:39 PM John Stone,
> <[2][6]johns_at_ks.uiuc.edu> wrote:
> >
> >Â Â Â Â Hi,
> >Â Â Â Â Ä*Â Axel's description is accurate.Ä*
> >
> >Â Â Â Â How many bonds do you actually need per-atom?Ä*
> >Â Â Â Â If you're running Linux or MacOS, it is trivial for
> >Â Â Â Â me to make a special build with a larger maximum bond
> count and post
> >Â Â Â Â it
> >Â Â Â Â for you.Ä*Â If you're using Windows, the process of
> making a special
> >Â Â Â Â build
> >Â Â Â Â is very involved and it would cost me too much time to be
> worth the
> >Â Â Â Â trouble,
> >Â Â Â Â and in that case I'd offer to build you a Linux version
> instead, as
> >Â Â Â Â I'm
> >Â Â Â Â sure you can find a machine to run it on.Ä*Â In any
> case, I would need
> >Â Â Â Â to know
> >Â Â Â Â how many bonds you actually need.
> >
> >Â Â Â Â Best,
> >Â Â Â Â Ä*Â John Stone
> >Â Â Â Â Ä*Â [3][7]vmd_at_ks.uiuc.edu
> >
> >Â Â Â Â On Thu, Jun 27, 2019 at 08:31:22AM -0400, Axel Kohlmeyer
> wrote:
> >Â Â Â Â >Ä*Â Ä*Â this number is a compile time choice. so to
> have a VMD
> >Â Â Â Â executable with a
> >Â Â Â Â >Ä*Â Ä*Â larger allowance for the number of bonds per
> atom, you need to
> >Â Â Â Â compile a
> >Â Â Â Â >Ä*Â Ä*Â custom executable, which is a non-trivial task
> unless you are
> >Â Â Â Â familiar
> >Â Â Â Â >Ä*Â Ä*Â with compiling software with many dependencies
> and
> >Â Â Â Â unconventional build
> >Â Â Â Â >Ä*Â Ä*Â scripts and settings. if you are running on
> windows and need a
> >Â Â Â Â windows
> >Â Â Â Â >Ä*Â Ä*Â executable, it is particularly challenging.
> >Â Â Â Â >Ä*Â Ä*Â axel.
> >Â Â Â Â >Ä*Â Ä*Â On Thu, Jun 27, 2019 at 8:25 AM Wasim Abdul
> >Â Â Â Â >Ä*Â Ä*Â <[1][4][8]wasimorbrooklyn2013_at_gmail.com>
> wrote:
> >Â Â Â Â >
> >Â Â Â Â >Ä*Â Ä*Â Ä*Â I have the need to have many bonds per
> atoms as I want to
> >Â Â Â Â visualize a
> >Â Â Â Â >Ä*Â Ä*Â Ä*Â polymer network. I have used carbon as
> the atom name, but it
> >Â Â Â Â is actually
> >Â Â Â Â >Ä*Â Ä*Â Ä*Â a model system. I have a structure file
> ready, but VMD shows
> >Â Â Â Â the errors
> >Â Â Â Â >Ä*Â Ä*Â Ä*Â like the following for multiple atoms:
> >Â Â Â Â >Ä*Â Ä*Â Ä*Â MolAtom 77: Exceeded maximum number of
> bonds (12)
> >Â Â Â Â >Ä*Â Ä*Â Ä*Â Please help.
> >Â Â Â Â >
> >Â Â Â Â >Ä*Â Ä*Â --
> >Â Â Â Â >Ä*Â Ä*Â Dr. Axel Kohlmeyer Ã**
> [2][5][9]akohlmey_at_gmail.com Ã**
> >Â Â Â Â [3][6][10]http://goo.gl/1wk0
> >Â Â Â Â >Ä*Â Ä*Â College of Science & Technology, Temple
> University,
> >Â Â Â Â Philadelphia PA, USA
> >Â Â Â Â >Ä*Â Ä*Â International Centre for Theoretical Physics,
> Trieste. Italy.
> >Â Â Â Â >
> >Â Â Â Â > References
> >Â Â Â Â >
> >Â Â Â Â >Ä*Â Ä*Â Visible links
> >Â Â Â Â >Ä*Â Ä*Â 1. mailto:[7][11]wasimorbrooklyn2013_at_gmail.com
> >Â Â Â Â >Ä*Â Ä*Â 2. mailto:[8][12]akohlmey_at_gmail.com
> >Â Â Â Â >Ä*Â Ä*Â 3. [9][13]http://goo.gl/1wk0
> >
> >Â Â Â Â --
> >Â Â Â Â NIH Center for Macromolecular Modeling and Bioinformatics
> >Â Â Â Â Beckman Institute for Advanced Science and Technology
> >Â Â Â Â University of Illinois, 405 N. Mathews Ave, Urbana, IL
> 61801
> >Â Â Â Â [10][14]http://www.ks.uiuc.edu/~johns/Ä*Â Ä*Â Ä*Â Ä*Â
> Ä*Â Ä* Phone: 217-244-3349
> >Â Â Â Â [11][15]http://www.ks.uiuc.edu/Research/vmd/Ä*Â Ä*Â Ä*
> >
> > References
> >
> >Â Â Visible links
> >Â Â 1. mailto:[16]wasimorbrooklyn2013_at_gmail.com
> >Â Â 2. mailto:[17]johns_at_ks.uiuc.edu
> >Â Â 3. mailto:[18]vmd_at_ks.uiuc.edu
> >Â Â 4. mailto:[19]wasimorbrooklyn2013_at_gmail.com
> >Â Â 5. mailto:[20]akohlmey_at_gmail.com
> >Â Â 6. [21]http://goo.gl/1wk0
> >Â Â 7. mailto:[22]wasimorbrooklyn2013_at_gmail.com
> >Â Â 8. mailto:[23]akohlmey_at_gmail.com
> >Â Â 9. [24]http://goo.gl/1wk0
> >Â Â 10. [25]http://www.ks.uiuc.edu/~johns/
> >Â Â 11. [26]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
> [27]http://www.ks.uiuc.edu/~johns/Â Â Â Â Â Â Phone: 217-244-3349
> [28]http://www.ks.uiuc.edu/Research/vmd/Â Â Â
>
> References
>
> Visible links
> 1. mailto:wasimorbrooklyn2013_at_gmail.com
> 2. mailto:johns_at_ks.uiuc.edu
> 3. http://www.ks.uiuc.edu/Research/vmd/alpha/256bonds/vmd-1.9.4a34.bin.LINUXAMD64.opengl.tar.gz
> 4. mailto:vmd_at_ks.uiuc.edu
> 5. mailto:wasimorbrooklyn2013_at_gmail.com
> 6. mailto:johns_at_ks.uiuc.edu
> 7. mailto:vmd_at_ks.uiuc.edu
> 8. mailto:wasimorbrooklyn2013_at_gmail.com
> 9. mailto:akohlmey_at_gmail.com
> 10. http://goo.gl/1wk0
> 11. mailto:wasimorbrooklyn2013_at_gmail.com
> 12. mailto:akohlmey_at_gmail.com
> 13. http://goo.gl/1wk0
> 14. http://www.ks.uiuc.edu/~johns/%C4%80
> 15. http://www.ks.uiuc.edu/Research/vmd/%C4%80
> 16. mailto:wasimorbrooklyn2013_at_gmail.com
> 17. mailto:johns_at_ks.uiuc.edu
> 18. mailto:vmd_at_ks.uiuc.edu
> 19. mailto:wasimorbrooklyn2013_at_gmail.com
> 20. mailto:akohlmey_at_gmail.com
> 21. http://goo.gl/1wk0
> 22. mailto:wasimorbrooklyn2013_at_gmail.com
> 23. mailto:akohlmey_at_gmail.com
> 24. http://goo.gl/1wk0
> 25. http://www.ks.uiuc.edu/~johns/
> 26. http://www.ks.uiuc.edu/Research/vmd/
> 27. http://www.ks.uiuc.edu/~johns/
> 28. 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/