VMD-L Mailing List

From: Wasim Abdul (wasimorbrooklyn2013_at_gmail.com)
Date: Fri Jul 12 2019 - 04:38:31 CDT

Hi John,
I tried the build. It works perfectly. Thank you guys so so much!

Sincerely,
Wasim

On Thu, Jul 11, 2019 at 2:24 AM John Stone <johns_at_ks.uiuc.edu> wrote:

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