From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Fri May 02 2008 - 01:25:35 CDT
There is currently no GUI for cionize. In the VMD console, try running
'package require cionize' and then 'cionize'. If you look at the plugins
directory under your VMD installation path, you will find both the
stand-alone binary as well as the current documentation (which should
make it to the VMD website soon).
On Fri, May 02, 2008 at 04:06:48PM +1000, Swarna Patra wrote:
> I have downloaded and installed vmd 1.8.7a23, I was looking under modelling
> cionize but didn't find. is there any documentation to where and how to run
> On Friday 02 May 2008 14:47, Leonardo Trabuco wrote:
> > Hi,
> > Here are instructions on how to download VMD test versions, which
> > include cionize:
> > http://www.ks.uiuc.edu/Research/vmd/alpha/
> > A pre-compiled version for Linux should do just fine for you.
> > And no, meadionize is not the same as cionize. Meadionze places ions at
> > minimia of an electrostatic potential calculated with MEAD, a
> > Poisson-Boltzmann solver. Cionize iteratively places ions at minima of
> > the Coulomb potential.
> > Cheers,
> > Leo
> > On Fri, May 02, 2008 at 11:04:47AM +1000, Swarna Patra wrote:
> > > Hi Leo
> > > could you pl give me the link for 'cionize'. I got meadionize is it the
> > > same? I have some problem in compiling. I am on suse linux machine and
> > > using gcc 4.1.2 version
> > > thanks
> > > swarna
> > >
> > > On Friday 02 May 2008 02:32, Leonardo Trabuco wrote:
> > > > Hi Swarna,
> > > >
> > > > You should use the 'cionize' program instead, which implements the same
> > > > algorithm but is *much* more efficient. It also supports multithreading
> > > > and GPU acceleration. It is distributed as a VMD plugin in the latest
> > > > test versions.
> > > >
> > > > Cheers,
> > > > Leo
> > > >
> > > > On Thu, May 01, 2008 at 02:32:45PM +1000, Swarna Patra wrote:
> > > > > Hi
> > > > > I am trying to compile sodium.c program available in namd site under
> > > > > MDtools and then under sodium. I am getting compilation error as
> > > > > follows tmp/ccdoTSKp.o: In function `main':
> > > > > sodium-1.c:(.text+0x257): warning: the `gets' function is dangerous
> > > > > and should not be used.
> > > > > sodium-1.c:(.text+0x843): undefined reference to `nint'
> > > > > sodium-1.c:(.text+0x85f): undefined reference to `nint'
> > > > > sodium-1.c:(.text+0x87b): undefined reference to `nint'
> > > > > sodium-1.c:(.text+0x959): undefined reference to `sqrt'
> > > > > collect2: ld returned 1 exit status
> > > > >
> > > > >
> > > > > I tried to send e-mail to the address given, it doesn't work. If
> > > > > anyone has used it please let me know.
> > > > > thanks
> > > > > swarna
-- Leonardo Trabuco, Ph.D. student Theoretical and Computational Biophysics Group University of Illinois at Urbana-Champaign
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