VMD-L Mailing List

From: Chris Knorowski (cdknorow_at_iastate.edu)
Date: Wed Aug 31 2011 - 15:35:04 CDT

Here is the test file.

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

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