VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue May 22 2012 - 18:02:31 CDT

Hi,
  You are correct that the existing implementation requires all of
the frames to be loaded. There isn't any way to work around this except
to write your own analysis script that works one frame at a time. One
of the features I am working on for a future version of VMD is out-of-core
trajectory access, which would allow you to do this and other analyses
in a manner similar to the way BigDCD works, but it will support all of
the features that need all of the referenced frames to be loaded as well.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, May 21, 2012 at 10:39:45AM -0400, Raul Araya wrote:
> Dear VMD users
>
> Is there a way to use the measure rmsf command within the framework of
> bigdcd?
> I ask this because I know that the rmsf command will use avpos to
> calculate the average position of each atom...to do this I imagine that
> vmd requires to whole or at least the desired part of the trajectory to be
> loaded in the memory in order to be able to compute the average position.
> Thus, I think this will not work using bigdcd unless one includes in the
> measuring script some way to store the average position. How can this be
> accomplished?
>
> Thanks...
>
> Raul Araya Secchi
> B.Sc Molecular Biotechnology.
> Molecular Biotechnology Engineer.
> PhD Student (Biotechnology Program. UNAB, Chile)
> Computational Biology Lab (DLab)
> Center for Mathematical Modeling (CMM)
> Facultad de Ciencias Fisicas y Matematicas.
> Universidad de Chile. 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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