VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Feb 25 2014 - 07:51:59 CST

P.S.: there are some interesting things that you can do by customizing
your .vmdrc file, beyond what is in the user's guide. check out:
https://sites.google.com/site/akohlmey/random-hacks/vmd-initialization-scripts

axel.

On Tue, Feb 25, 2014 at 8:49 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> .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.
>> 

-- 
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.