Re: compilaton error

From: Swarna Patra (swarna_at_physics.usyd.edu.au)
Date: Fri May 02 2008 - 01:06:48 CDT

Hi
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
it?
thanks
swarna
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

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