VMD-L Mailing List

From: Marc Baaden (baaden_at_smplinux.de)
Date: Tue Jan 17 2012 - 12:08:31 CST

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