From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 17 2012 - 12:19:40 CST

Marc,
  If you would like to play around with it, I can make you a
special build that has the necessary modifications turned on...
This functionality will eventually be in the standard version of
VMD, but I still have to make many changes to the core of VMD
to fully support the out-of-core trajectory access scheme in such
a way that it works for visualization and so that it also works
transparently for all Tcl/Python scripting and for the various
built-in VMD analysis functions in VMD. The modified version of
VMD I created for that paper only implements enough of the
infrastructure to support the visualization-related use cases
so far. The standard builds of VMD already benefit from the
changes I made for the SSD-optimized I/O mechanism. The part
that remains to be completed the out-of-core feature shows up in
production versions of VMD is the abstraction layer that emulates
the familiar "in-core" trajectory behavior VMD provides to the
user, while transparently pulling frames from disk on-the-fly.

Anyway, after I get done with releasing VMD 1.9.1, I would be happy
to provide you with some test builds you can play with that allow
out-of-core visualization. This modified version should also work
for "BigDCD" style analysis runs, but it doesn't implement the full
out-of-core abstraction layer I describe above.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jan 17, 2012 at 07:08:31PM +0100, Marc Baaden wrote:
>
> Dear John (cc to vmd-list),
>
> I enjoyed your recent paper on "Immersive out-of-core visualization of
> large-size and long-timescale molecular dynamics trajectories". This is
> an issue that we are also struggling with here in the lab, and I wonder
> whether there may be a development/beta version of VMD with such
> features available for testing.
>
> It's also not clear to me whether this is just an extension (plugin?)
> to VMD, or an intrinsically different/separate build.
>
> Thank you very much in advance,
> Marc
>
>
> johns_at_ks.uiuc.edu said:
> >> John E. Stone, Kirby L. Vandivort, and Klaus Schulten. Immersive
> >> out-of-core visualization of large-size and long-timescale molecular
> >> dynamics trajectories. Lecture Notes in Computer Science, 6939:1-12,
> >> 2011. (PMC: 3032211) Atomistic molecular dynamics (MD) simulations of
> >> biomolecules provide insight into their physical mechanisms and
> >> potential as drug targets. Unfortunately, such simulations are
> >> extremely demanding in terms of computation, storage, and
> >> visualization. Immersive visualization environments permit fast,
> >> intuitive exploration of the pharmacological potential, but add
> >> further demands on resources. We describe the design and application
> >> of out-of-core visualization techniques for large-size and
> >> longtimescale MD simulations involving many terabytes of data,
> >> including in particular fast regeneration of molecular representations
> >> , atom selection mechanisms, out-of-core optimized MD trajectory file
> >> formats, and multithreaded programming techniques. Our approach
> >> leverages technological advances in commodity solid state disk (SSD)
> >> devices, to enable trajectory animation rates for large structures
> >> that were previously unachievable except by in-core approaches, while
> >> maintaining full visualization flexibility. The out-of-core
> >> visualization techniques are implemented and evaluated in VMD, a
> >> widely used molecular visualization tool.
>
>
> --
> Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris
> mailto:baaden_at_smplinux.de - http://www.baaden.ibpc.fr
> FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217
>
>

-- 
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Beckman Institute for Advanced Science and Technology
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