VMD-L Mailing List

From: Wasim Abdul (wasimorbrooklyn2013_at_gmail.com)
Date: Fri Jun 28 2019 - 01:42:49 CDT

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 using
carbon as the atom for a bead of the polymer.
Thank you.

On Thu, Jun 27, 2019 at 7:40 PM Wasim Abdul <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, <johns_at_ks.uiuc.edu> wrote:
>
>> Hi,
>> Axel's description is accurate.
>>
>> How many bonds do you actually need per-atom?
>> 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,
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>> On Thu, Jun 27, 2019 at 08:31:22AM -0400, Axel Kohlmeyer wrote:
>> > this number is a compile time choice. so to have a VMD executable
>> with a
>> > larger allowance for the number of bonds per atom, you need to
>> compile a
>> > custom executable, which is a non-trivial task unless you are
>> familiar
>> > with compiling software with many dependencies and unconventional
>> build
>> > scripts and settings. if you are running on windows and need a
>> windows
>> > executable, it is particularly challenging.
>> > axel.
>> > On Thu, Jun 27, 2019 at 8:25 AM Wasim Abdul
>> > <[1]wasimorbrooklyn2013_at_gmail.com> wrote:
>> >
>> > I have the need to have many bonds per atoms as I want to
>> visualize a
>> > polymer network. I have used carbon as the atom name, but it is
>> actually
>> > a model system. I have a structure file ready, but VMD shows the
>> errors
>> > like the following for multiple atoms:
>> > MolAtom 77: Exceeded maximum number of bonds (12)
>> > Please help.
>> >
>> > --
>> > Dr. Axel Kohlmeyer Ā [2]akohlmey_at_gmail.com Ā [3]http://goo.gl/1wk0
>> > College of Science & Technology, Temple University, Philadelphia PA,
>> USA
>> > International Centre for Theoretical Physics, Trieste. Italy.
>> >
>> > References
>> >
>> > Visible links
>> > 1. mailto:wasimorbrooklyn2013_at_gmail.com
>> > 2. mailto:akohlmey_at_gmail.com
>> > 3. 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
>> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
>> http://www.ks.uiuc.edu/Research/vmd/
>>
>