VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Oct 26 2015 - 15:39:37 CDT

On Mon, Oct 26, 2015 at 4:06 PM, Aris Marcolongo <aris.marcolongo_at_gmail.com>
wrote:

> No clue? Is there an other simple way to leave the track of the motion of
> selected atoms using VMD?
>

​the script you are pointing to works as documented​, but the command it
defines is called "trajectory_path" and not "traj".
the error message you quote does not make sense with the script you quoted.
it cannot generate this error.

PEBCAC?

axel.

>
> Thanks,
>
> Aris
>
>
> 2015-10-26 12:02 GMT+01:00 Aris Marcolongo <aris.marcolongo_at_gmail.com>:
>
>> Hello,
>>
>> I am trying to use this script:
>>
>>
>> http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/trajectory_path/ <https://ewa.epfl.ch/owa/redir.aspx?SURL=-XIwpi3phwsVq54Qgbd-NJ_5lkgmK5aQGTkckEriak_bdi6o9N3SCGgAdAB0AHAAOgAvAC8AdwB3AHcALgBrAHMALgB1AGkAdQBjAC4AZQBkAHUALwBSAGUAcwBlAGEAcgBjAGgALwB2AG0AZAAvAHMAYwByAGkAcAB0AF8AbABpAGIAcgBhAHIAeQAvAHMAYwByAGkAcAB0AHMALwB0AHIAYQBqAGUAYwB0AG8AcgB5AF8AcABhAHQAaAAvAA..&URL=http%3a%2f%2fwww.ks.uiuc.edu%2fResearch%2fvmd%2fscript_library%2fscripts%2ftrajectory_path%2f>
>>
>>
>> for visualizing the trajectory of a single atom with VMD,
>> here with index 59. I am a beginner with VMD, and I just wrote in
>> the TkC console:
>>
>> > source traj.tcl
>> > set crystal [atomselect top "index 59"]
>> atomselect11
>> > traj $crystal scale
>>
>> but I finally end up with the error.
>>
>> Illegal molecule specification 'index 59': Could not
>> find molecule 'index 59'. mol new operates on one molecule only
>>
>> How can I solve this problem?
>>
>>
>> Thanks a lot for any help,
>>
>>
>> Aris
>>
>>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.