VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jan 26 2009 - 15:55:29 CST

Nicholas,
  It works fine for me if I display the structure using VDW for
selection "all", and then create a second representation (also "all")
for DynamicBonds, with the default parameters. What version of VMD
are you using, and which version of the LAMMPS plugin do you have
installed? Be as detailed as possible, as it will help me figure out
what's going wrong there. I'm able to animate a movie of your LAMMPS
trajectory and the bonds appear to be computed and displayed correctly
for me. I'm guessing you've been using a VMD build with a much older
version of the LAMMPS plugin which has had lots of improvements made
in the last year and a half.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jan 21, 2009 at 11:11:39AM -0600, nicholas lee wrote:
> Hi John,
>
> I am resending my last email because I am not sure if it went through. I apologize if you receive this twice.
>
> > Can you send me your LAMMPS files so I can have a look?
>
> Yes. I believe the file may have been to large to send by e-mail. You can download it from the link below.
>
> http://www.njolee.net/show/test.lammpstrj
>
> I am only concerned with showing bonds between the atoms in the parallel tubes (labeled type 1 in the file). The other atoms, labeled type 2, are fine as they are. I really appreciate your help John.
>
> Regards,
>
> Nicholas J. Lee
>
>
>
>
>
>
>
>
> On Tue, Jan 20, 2009 at 5:26 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> > Hi,
> > Can you send me your LAMMPS files so I can have a look?
> > There may be some other reason that it's not bonding your atoms.
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Tue, Jan 20, 2009 at 03:01:16PM -0600, nicholas lee wrote:
> >> Thanks John,
> >>
> >> But I still must be doing something wrong. Screenshots of what I am expecting are shown at the links below.
> >>
> >> http://www.njolee.net/show/CPK.JPG
> >> Here, I have loaded the molecule configuration from the TK console, entering source->mol-> lmpbondsfromdata,etc. I want the interatomic bonds break but they do not.
> >>
> >> http://www.njolee.net/show/CPK2.JPG
> >> Here, I have simply loaded the molecule configuration by double-clicking my lammpstrj file. I want to connect the gray atoms using the "dynamic bonds" representation but they never connect, no matter how large i set the cut-off bond length.
> >>
> >> In both cases, when I switch from "CPK" to "DynamicBonds" representation, my atoms disappear and I get a blank display window shown at this link.
> >>
> >> http://www.njolee.net/show/Dynamicbonds.JPG
> >>
> >> Maybe you can have a look at my settings in the screenshots....Thanks again for your help.
> >>
> >> Nicholas J. Lee
> >>
> >> More details: From the User's Guide, it seems as if I have made all the necessary selections in the menu
> >> and that there is nothing more I need to do other than provide my geometry data.
> >>
> >> http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.6/ug/node53.html#4064
> >> http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.6/ug/node52.html#ug:topic:drawmethods:bonds
> >> http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.6/ug/node56.html#ug:topic:drawmethods:vdw
> >>
> >> On Tue, Jan 20, 2009 at 10:47 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
> >> >
> >> > Hi,
> >> > Use the "DynamicBonds" representation in combination with the VDW or
> >> > other representations, and you should be able to get what you want.
> >> >
> >> > Cheers,
> >> > John Stone
> >> > vmd_at_ks.uiuc.edu
> >> >
> >> > On Tue, Jan 20, 2009 at 10:40:46AM -0600, nicholas lee wrote:
> >> >> Hi,
> >> >>
> >> >> I want to show bonds breaking when stretched beyond a specified cut-off distance in VMD. What "Drawing Method" should I use? An example of what I would like to see is below.
> >> >>
> >> >> http://njolee.net/show/eqvide.mpg
> >> >>
> >> >> Thanks,
> >> >>
> >> >> Nicholas J. Lee
> >> >>
> >> >> More details: I am creating movies from LAMMPS trajectory files. I know how to create bond geometries from bond topology files (using source->mol->lmpbondsfromdata,etc), but this is not what I want, because they use fixed topologies. When bond topology is fixed, bonds are drawn between atoms no matter how far they move apart. I do not want this. I want bonds to be drawn only if the distance between atoms is less than a number I specify as shown in the movie above.
> >> >>
> >> >>
> >> >
> >> > --
> >> > NIH Resource for Macromolecular Modeling and Bioinformatics
> >> > Beckman Institute for Advanced Science and Technology
> >> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> >> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> >> >
> >
> > --
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> > 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078