VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue May 22 2012 - 18:53:22 CDT

On Tue, May 22, 2012 at 7:02 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> 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

john,

how about adding an option to feed a set of
averaged positions to the measure rmsf command?

then this could be done in a two pass bigdcd procedure.
and for file formats that your out-of-core stuff won't
support (initially or ever).

just an idea...
     axel.

> 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
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.