VMD-L Mailing List

From: daniel aguayo (bioquimico_at_gmail.com)
Date: Mon Aug 17 2009 - 19:28:30 CDT

I'll have my sytem ready for the ionization on friday. I'll will send you
the info asap

DAV

On Mon, Aug 17, 2009 at 2:49 PM, John Stone<johns_at_ks.uiuc.edu> wrote:
>
> 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
> 

-- 
saludos desde el fin del mundo