VMD-L Mailing List

From: Wasim Abdul (wasimorbrooklyn2013_at_gmail.com)
Date: Fri Jun 28 2019 - 13:47:04 CDT

Thank you so so much. I'll try it and let you know.

On Fri 28 Jun, 2019, 9:50 PM John Stone, <johns_at_ks.uiuc.edu> wrote:

> 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 usingĀ
> > 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
> > letĀ 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,
> > Ā Axel's description is accurate.Ā
> >
> > How many bonds do you actually need per-atom?Ā
> > 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.Ā 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.Ā In any case, I would
> need
> > to know
> > how many bonds you actually need.
> >
> > Best,
> > Ā John Stone
> > Ā [3]vmd_at_ks.uiuc.edu
> >
> > On Thu, Jun 27, 2019 at 08:31:22AM -0400, Axel Kohlmeyer wrote:
> > >Ā Ā this number is a compile time choice. so to have a VMD
> > executable with a
> > >Ā Ā larger allowance for the number of bonds per atom, you
> need to
> > compile a
> > >Ā Ā custom executable, which is a non-trivial task unless you
> are
> > familiar
> > >Ā Ā with compiling software with many dependencies and
> > unconventional build
> > >Ā Ā scripts and settings. if you are running on windows and
> need a
> > windows
> > >Ā Ā executable, it is particularly challenging.
> > >Ā Ā axel.
> > >Ā Ā On Thu, Jun 27, 2019 at 8:25 AM Wasim Abdul
> > >Ā Ā <[1][4]wasimorbrooklyn2013_at_gmail.com> wrote:
> > >
> > >Ā Ā Ā I have the need to have many bonds per atoms as I want
> to
> > visualize a
> > >Ā Ā Ā polymer network. I have used carbon as the atom name,
> but it
> > is actually
> > >Ā Ā Ā a model system. I have a structure file ready, but VMD
> shows
> > the errors
> > >Ā Ā Ā like the following for multiple atoms:
> > >Ā Ā Ā MolAtom 77: Exceeded maximum number of bonds (12)
> > >Ā Ā Ā Please help.
> > >
> > >Ā Ā --
> > >Ā Ā Dr. Axel Kohlmeyer Ä* [2][5]akohlmey_at_gmail.com Ä*
> > [3][6]http://goo.gl/1wk0
> > >Ā Ā College of Science & Technology, Temple University,
> > Philadelphia PA, USA
> > >Ā Ā International Centre for Theoretical Physics, Trieste.
> Italy.
> > >
> > > References
> > >
> > >Ā Ā Visible links
> > >Ā Ā 1. mailto:[7]wasimorbrooklyn2013_at_gmail.com
> > >Ā Ā 2. mailto:[8]akohlmey_at_gmail.com
> > >Ā Ā 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/Ā Ā Ā Ā Ā Ā Phone:
> 217-244-3349
> > [11]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. 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/
>