From: Ye Yang (knightyangpku_at_gmail.com)
Date: Mon Aug 01 2011 - 11:36:26 CDT
i, all,
I get the cionize running, yet I met another problem.
When I use the cionize and only input the -mol molecular id, it seems
to be calculating the grid, yet I can find nowhere the output of charge
coordinate, nor did any charge added to the system.
If I wrote a configuration file and do as the instruction of
http://www.ks.uiuc.edu/Research/vmd/plugins/cionize/
I will receive the message "Not valid molecule id in atomselect's
'molId" if I do not specify -mol
If I specify molecular ID, it seems all other inputs (including
specifying the number of processors will be ignored.)
Also, one thing I noticed is that the instruction from the webpage is
not the same as the instruction in the Tk console (by type in
::cionize::cionize)
It seems that I have to use cionize outside of vmd and manually write
configuration file each time
Is there any way I solve this?
Thank you very much.
Ye
2011/7/29 Axel Kohlmeyer <akohlmey_at_gmail.com>
> On Fri, Jul 29, 2011 at 12:17 PM, Ye Yang <knightyangpku_at_gmail.com> wrote:
> > Hi, all:
> > I am simulation DNA/protein system.
> > According to the autoionization instruction, it is not recommended
> to
> > use this, so I want to use cionize plugin instead.
> > However, I cannot use the cionize plugin successfully,
> > When I type in package require cionize, it looks fine and showed the
> > version 1.0
> > However, after this, if I type in cionize, instead of showing the
> > options, it always says " invalid command "cionize""
>
> in addition to "requiring" the plugin, you also
> need to either import the exported commands
> from the plugin's namespace. e.g. add:
>
> namespace import ::cionize::*
>
> or just use:
>
> ::cionize::cionize
>
> cheers,
> axel.
>
> > Does anyone know how to use this plugin? Would anyone please provide
> me
> > with an example?
> > Thank you very much.
> >
> > Ye
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>
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