VMD-L Mailing List

From: Wasim Abdul (wasimorbrooklyn2013_at_gmail.com)
Date: Wed Jul 03 2019 - 01:09:12 CDT

Hi John,
These errors are appearing when I try to start vmd:
OptiXRenderer) ERROR: Failed to load the OptiX shared library.
OptiXRenderer) NVIDIA driver may be too old.
OptiXRenderer) 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 <wasimorbrooklyn2013_at_gmail.com>
wrote:

> 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/
>>
>