VMD-L Mailing List

From: nicholas lee (nicholjl_at_usc.edu)
Date: Tue Jan 20 2009 - 15:01:16 CST

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
>