VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Oct 19 2009 - 15:27:43 CDT

Joshua,
  I should have a new test build posted on biocore late this week.
I've been working hard on adding basic OpenCL infrastructure and the
first couple of OpenCL kernels into VMD and as a result I've been
spending a fair amount of my time working around various small bugs
in the beta OpenCL implementations I'm working with presently.
I'll should have fresh test builds posted on Thursday if all goes well.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Oct 18, 2009 at 11:19:28PM -0400, Joshua Adelman wrote:
> Hi Leo,
>
> Thanks for your response. Any idea of when the new build might be
> posted on biocore? I can probably get access to a linux machine, but
> it would definitely be easier to have a working os x version.
>
> Josh
>
> On Oct 17, 2009, at 4:26 PM, Leonardo Trabuco wrote:
>
> >Dear Joshua,
> >
> >On Fri, Oct 16, 2009 at 4:20 PM, Joshua Adelman <jla65_at_pitt.edu>
> >wrote:
> >>I am attempting to use the MDFF plugin that is available in the
> >>development
> >>version of VMD. I downloaded VMD 1.8.8a1 for Intel-based OSX
> >>machines from
> >>Biocore. As a side note, the disk image is named properly, but for
> >>some
> >>reason the name of the vmd app is named 1.8.7 (when running VMD it
> >>displays
> >>the correct version number though).
> >
> >Right, John Stone is aware that he needs to change the disk image for
> >the next Mac builds. :-)
> >
> >>After issuing the "require package mdff" commend (returns version
> >>0.2), I
> >>attempt to build a simulated map using "mdff sim". When I issue the
> >>tcl
> >>command, I get a pop-up window:
> >>"Could not locate '/Applications/VMD'"
> >>
> >>And then it asks if I'd like to identify the path. When I select
> >>the VMD
> >>app, I get a warning that '/Application/VMD 1.8.8a1.app' is not
> >>executable.
> >>
> >>The mdff sim routine still runs, but it fails when it tries to make
> >>use of
> >>volutil (I assume this is what it needs to identify the VMD app in
> >>order to
> >>find it). I don't get any further error messages, but basically it
> >>never
> >>completes the low-pass filtering step, because it doesn't know
> >>where volutil
> >>lives.
> >
> >We are also aware of this problem, but haven't got around preparing a
> >new build addressing it yet. According to John, we need to fix the
> >plugin builds so they use the path-relative Tcl library if they are
> >compiled against the VMD Tcl library rather than the system-provided
> >one.
> >
> >>Any suggestions would be most appreciated.
> >
> >Please wait until a new Mac build is posted on biocore. Or, if you
> >can, give the Linux version a try for now.
> >
> >Thanks,
> >Leo
> >
> >>Josh
> >>
> >>
> >>
> >>
> >>
> >
> >
> >
> >--
> >Leonardo Trabuco, Ph.D. candidate
> >Theoretical and Computational Biophysics Group
> >University of Illinois at Urbana-Champaign 

-- 
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