VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Aug 17 2009 - 13:49:09 CDT

Daniel,
  Let me know how it works for you when you've had a chance to use it.

I have a tiny update to apply to the source code to address a small bug that
crops up with the latest version of CUDA, but it may not affect you if you're
using cionize for normal ion placement and not for time-averaged potential
maps of trajectories (a somewhat obscure additional feature of cionize...)

Cheers,
  John

On Tue, Aug 11, 2009 at 02:16:04PM -0400, daniel aguayo wrote:
> Tks a lot John
> :P
>
> My bests
>
> Daniel
>
> On Thu, Aug 6, 2009 at 3:48 PM, John Stone<johns_at_ks.uiuc.edu> wrote:
> >
> > Hi,
> >  I've posted a MacOS X binary of cionize for you here:
> > http://www.ks.uiuc.edu/Research/vmd/alpha/cionize/
> >
> > To run it, gunzip it, then see the README file that I put
> > in that directory as well.  Let me know if you need help
> > using it or if you run into any problems.
> >
> > I should mention that VMD is beginning to incorporate the
> > computation routines used by cionize, and we'll probably completely
> > replace cionize with VMD scripts in the next 6 months or so.
> > All that remains is to write new VMD routines to do the electrostatic
> > map "update" steps that cionize does after placing each ion.  Once
> > that's in place, you'll be able to write a short VMD script that does
> > everything that cionize does.
> >
> > Cheers,
> >  John Stone
> >  vmd_at_ks.uiuc.edu
> >
> > On Wed, Aug 05, 2009 at 09:46:10PM -0400, daniel aguayo wrote:
> >> Tks John, I'll be waiting for it.
> >> Cheers
> >> DAV
> >>
> >> On Wed, Aug 5, 2009 at 9:43 PM, John Stone<johns_at_ks.uiuc.edu> wrote:
> >> >
> >> > Hi,
> >> >  I will be compiling updated versions of catdcd and cionize based
> >> > on the latest VMD plugins.  I should be able to provide CUDA-enabled
> >> > Mac builds of cionize shortly.
> >> >
> >> > Cheers,
> >> >  John Stone
> >> >  vmd_at_ks.uiuc.edu
> >> >
> >> > On Wed, Aug 05, 2009 at 09:29:07PM -0400, daniel aguayo wrote:
> >> >> I want to use de cionize plugin on vmd 1.8.7, but I can't find de
> >> >> cionize executable?
> >> >> I tried to compile it from the source version on my mac leopard, but I can't.
> >> >> Anyone can help me.
> >> >>
> >> >> Tks a lot
> >> >>
> >> >> Daniel Aguayo V.
> >> >> Centro de Bionformatica y Simulacion Molecular
> >> >> Universidad de Talca
> >> >> Chile
> >> >>
> >> >> --
> >> >> saludos desde el fin del mundo
> >> >
> >> > --
> >> > NIH Resource for Macromolecular Modeling and Bioinformatics
> >> > Beckman Institute for Advanced Science and Technology
> >> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >> > Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
> >> >  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078
> >> >
> >>
> >>
> >>
> >> --
> >> saludos desde el fin del mundo
> >
> > --
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
> >  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078
> >
>
>
>
> --
> saludos desde el fin del mundo 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078