VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jun 28 2019 - 11:20:52 CDT

Hi Wasim,
  I've posted a 256-bond-per-atom test build for you here.
Please try it, and let me know if that resolves your max bond count
problem or not:
  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,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jun 28, 2019 at 12:12:49PM +0530, Wasim Abdul wrote:
> Hi John,
> I have a maximum of 221 bonds for one of the beads of the polymer. Can a
> maximum limit of 250 be set? I'm usingÂ
> carbon as the atom for a bead of the polymer.
> Thank you.
> On Thu, Jun 27, 2019 at 7:40 PM Wasim Abdul
> <[1]wasimorbrooklyn2013_at_gmail.com> wrote:
>
> I'm using Linux. I'll count the maximum number of bonds I have and
> let you know. Thank you so so much.
> On Thu 27 Jun, 2019, 7:39 PM John Stone, <[2]johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> Â Axel's description is accurate.Â
>
> How many bonds do you actually need per-atom?Â
> If you're running Linux or MacOS, it is trivial for
> me to make a special build with a larger maximum bond count and post
> it
> for you. If you're using Windows, the process of making a special
> build
> is very involved and it would cost me too much time to be worth the
> trouble,
> and in that case I'd offer to build you a Linux version instead, as
> I'm
> sure you can find a machine to run it on. In any case, I would need
> to know
> how many bonds you actually need.
>
> Best,
> Â John Stone
> Â [3]vmd_at_ks.uiuc.edu
>
> On Thu, Jun 27, 2019 at 08:31:22AM -0400, Axel Kohlmeyer wrote:
> >Â Â this number is a compile time choice. so to have a VMD
> executable with a
> >Â Â larger allowance for the number of bonds per atom, you need to
> compile a
> >Â Â custom executable, which is a non-trivial task unless you are
> familiar
> >Â Â with compiling software with many dependencies and
> unconventional build
> >Â Â scripts and settings. if you are running on windows and need a
> windows
> >Â Â executable, it is particularly challenging.
> >Â Â axel.
> >Â Â On Thu, Jun 27, 2019 at 8:25 AM Wasim Abdul
> >Â Â <[1][4]wasimorbrooklyn2013_at_gmail.com> wrote:
> >
> >Â Â Â I have the need to have many bonds per atoms as I want to
> visualize a
> >Â Â Â polymer network. I have used carbon as the atom name, but it
> is actually
> >Â Â Â a model system. I have a structure file ready, but VMD shows
> the errors
> >Â Â Â like the following for multiple atoms:
> >Â Â Â MolAtom 77: Exceeded maximum number of bonds (12)
> >Â Â Â Please help.
> >
> >Â Â --
> >Â Â Dr. Axel Kohlmeyer Ä* [2][5]akohlmey_at_gmail.com Ä*
> [3][6]http://goo.gl/1wk0
> >Â Â College of Science & Technology, Temple University,
> Philadelphia PA, USA
> >Â Â International Centre for Theoretical Physics, Trieste. Italy.
> >
> > References
> >
> >Â Â Visible links
> >Â Â 1. mailto:[7]wasimorbrooklyn2013_at_gmail.com
> >Â Â 2. mailto:[8]akohlmey_at_gmail.com
> >Â Â 3. [9]http://goo.gl/1wk0
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [10]http://www.ks.uiuc.edu/~johns/Â Â Â Â Â Â Phone: 217-244-3349
> [11]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. mailto:vmd_at_ks.uiuc.edu
> 4. mailto:wasimorbrooklyn2013_at_gmail.com
> 5. mailto:akohlmey_at_gmail.com
> 6. http://goo.gl/1wk0
> 7. mailto:wasimorbrooklyn2013_at_gmail.com
> 8. mailto:akohlmey_at_gmail.com
> 9. http://goo.gl/1wk0
> 10. http://www.ks.uiuc.edu/~johns/
> 11. 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/