From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Feb 25 2014 - 07:49:58 CST

.vmdrc goes into your home directory. Please read up on it in the VMD
user's guide.
...and make sure it contains menu main on.

Axel

On Feb 25, 2014 8:41 AM, "DanLiu" <Dan.Liu_at_simap.grenoble-inp.fr> wrote:
>
> Thanks, Axel.
> I just found a simple way for my case to ignore dummy atoms. Since the x
(or y, z) coordinate is never 0, so I just select 'all not x 0.0000'.
> And for the plugin, all files are in 'Read only', so it's not possible to
modify vmd.rc or vmd.py. Anyway, I'll work it under Win7 system, which is
parallel installed in my Mac. So it's not so inconvenient.
> Best wishes
> Dan
> On Feb 25, 2014, at 1:57 PM, Axel Kohlmeyer wrote:
>
> > On Tue, Feb 25, 2014 at 7:42 AM, DanLiu <Dan.Liu_at_simap.grenoble-inp.fr>
wrote:
> >> By the way, Axel, for visualization of lammps trajectory with variable
number of atoms, is it possible not displaying the dummy atoms in graphics?
> >
> > you can set the location with an environment variable. if you set one
> > coordinate to a very large value, say x=10000 the you can make a
> > selection x<10000 and they won't show.
> >
> > axel.
> >
> >> Thank you in advance.
> >> Best wishes
> >> Dan
> >> On Feb 25, 2014, at 12:56 PM, Axel Kohlmeyer wrote:
> >>
> >>> On Tue, Feb 25, 2014 at 6:18 AM, DanLiu <Dan.Liu_at_simap.grenoble-inp.fr>
wrote:
> >>>> Dear all,
> >>>> I've downloaded a new version of plugin. But I've no idea how to
update it. When I tried to replace the older one, system told me the VMD
file system is 'only read'.
> >>>> Does anybody know how to process it?
> >>>
> >>> best you talk to somebody local that is has expertise with the
> >>> unspecified operating system that you are using. this is not a VMD
> >>> issue directly.
> >>>
> >>> axel.
> >>>
> >>>> Thanks in advance
> >>>> Best wishes
> >>>> Dan
> >>>
> >>>
> >>>
> >>> --
> >>> 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.
> >>
> >
> >
> >
> > --
> > 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.
>