VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 20 2009 - 17:26:01 CST

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