Re: compilaton error

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Thu May 01 2008 - 23:47:06 CDT

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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