Re: namd-I: cionize problem in vmd

From: Ye Yang (
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
    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
    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.


2011/7/29 Axel Kohlmeyer <>

> On Fri, Jul 29, 2011 at 12:17 PM, Ye Yang <> 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
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.

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