VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Aug 31 2011 - 15:42:14 CDT

On Wed, Aug 31, 2011 at 4:35 PM, Chris Knorowski <cdknorow_at_iastate.edu> wrote:
> Here is the test file.

thanks a lot. i see why it might have confused an older version
of topotools. the current development version will stop
after the first frame, since your file doesn't follow the
"standard" xyz format: there is an extra empty line
after each configuration frame that must not be there.
once i remove that, the file loads fine and completely.

please have a look at the corrected version in the attachment.

cheers,
    axel.

> Chris
>
> On Wed, Aug 31, 2011 at 11:10 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>
>> chris,
>>
>> please always cc: the list. thanks.
>>
>> On Wed, Aug 31, 2011 at 12:05 PM, Chris Knorowski <cdknorow_at_iastate.edu>
>> wrote:
>> > Thanks Axel,
>> > I tried readvarxyz in topotools, but every time I attempted to load the
>> > file
>> > vmd froze up and the entire computer crashed. The file I was trying to
>> > load
>>
>> do you have vmd 1.9 and topotools 1.2?
>>
>> > was pretty small 10 frames, with a max of 50 particles.
>>
>> can you please send me a copy of that file off list,
>> if your vmd/topotools are up-to-date. you may have
>> triggered a bug and i'd like to have that squashed
>> rather than have people work around it.
>>
>> thanks,
>>    axel.
>>
>> > What I ended up doing is keeping all the dummy particles in but moving
>> > them
>> > to a location that is far away from the viewing screen when they were
>> > suppose to be gone.
>> >
>> > Chris
>> >
>> > On Mon, Aug 29, 2011 at 5:26 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
>> > wrote:
>> >>
>> >> On Mon, Aug 29, 2011 at 5:35 PM, Chris Knorowski <cdknorow_at_iastate.edu>
>> >> wrote:
>> >> > Is it possible to load a trajectory where the number of particles in
>> >> > each
>> >> > frame aren't conserved?
>> >> > I initially tried to load a trajectory in xyz format but vmd only
>> >> > loaded
>> >> > the
>> >> > first frame, I figured this was because the second had a different
>> >> > number of
>> >> > particles.
>> >>
>> >> nod. that is how VMD is designed.
>> >>
>> >> > Since this didn't work I tried something else as well. I kept the
>> >> > same
>> >> > number of particles, but changed the names of the ones that should
>> >> > be disappearing,
>> >> > for example:
>> >> > the first frame has 5 "Z" particles and 10 "M" particles. The second
>> >> > frame
>> >> > has 7 'Z' particles and 13 "M" particles. And then I wanted to
>> >> > show only
>> >> > the
>> >> > Z particles in each timestep.
>> >> >  However, it seems that vmd uses the names of the particles in the
>> >> > first
>> >> > frame and doesn't reupdate the name list as I step through time.
>> >>
>> >> nod. the names of all subsequent frames are completely ignored
>> >> and VMD assumes that particles remain the same over the course
>> >> of a trajectory.
>> >>
>> >> > Is there a way to force vmd to re-update the names at each timestep.
>> >> > Or
>> >> > make
>> >> > vmd load a trajectory with varying numbers of particles in each
>> >> > timestep.
>> >>
>> >> this is a recurring question. this is due to a fundamental design
>> >> decision,
>> >> which optimizes VMD performance and reduces its memory footprint for
>> >> the most common use cases. you can work around this with scripting.
>> >> one option to do this has been implemented in the topotools plugin:
>> >>
>> >>
>> >>
>> >> http://sites.google.com/site/akohlmey/software/topotools/topotools---documentation#TOC-readvarxyz-file-name-
>> >>
>> >> for other suggestions, please search the mailing list archives.
>> >>
>> >> cheers,
>> >>    axel.
>> >>
>> >>
>> >> > Thanks,
>> >> > Chris
>> >> >
>> >> >
>> >> > --
>> >> > Christopher Knorowski
>> >> >
>> >> > Iowa State Physics Department
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >> Dr. Axel Kohlmeyer
>> >> akohlmey_at_gmail.com  http://goo.gl/1wk0
>> >>
>> >> Institute for Computational Molecular Science
>> >> Temple University, Philadelphia PA, USA.
>> >
>> >
>> >
>> > --
>> > Christopher Knorowski
>> >
>> > Iowa State Physics Department
>> >
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer
>> akohlmey_at_gmail.com  http://goo.gl/1wk0
>>
>> Institute for Computational Molecular Science
>> Temple University, Philadelphia PA, USA.
>
>
>
> --
> Christopher Knorowski
>
> Iowa State Physics Department
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.