VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Feb 27 2013 - 16:05:25 CST

Max,
  Yes, that's the major benefit of the out-of-core implementation I'm
working on. It'll make it much more convenient to analyze arbitrarily
large datasets...

Cheers,
  John

On Wed, Feb 27, 2013 at 04:59:32PM -0500, Maximilian Ebert wrote:
> Hi,
> Thanks again. For now I will just use my code but indeed not to manage the
> trajectory loading would make many things easier. The feature will be
> super useful to many researchers I guess and make the whole analysis
> easier for less skilled users.
> Greets,
> Max
>
> Dipl.-Ing. Maximilian Ebert
>
> Etudiant au doctorat en biochimie
> Laboratoire du Dr. Joelle Pelletier
> Universite de Montreal
>
> m.ebert_at_umontreal.ca
> On 2013-02-27, at 11:34 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> I think that the BigDCD script is currently the easiest way to do
> the sort of analysis that you're describing, since you don't have to
> explicitly manage the trajectory loading process. I'm working on
> extending
> VMD to allow arbitrary out-of-core access to huge trajectory files
> without
> having to do things in either of the ways we've just discussed, but that
> feature is still a ways off yet.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Feb 26, 2013 at 05:35:54PM -0500, Maximilian Ebert wrote:
>
> Hi John,
>
> Thank you for your prompt answer. I am using mol load and mol delete
> to empty my RAM. The trajectory file is too large to load it
> completely. So I split it into smaller pieces to calculate the bfactor
> for the complete simulation. I load a 2GB DCD pull out the information
> of all frames, store them in an array, go to next fragment trajectory,
> do the same and finally calculate the bfactor.
>
> If there is a better way to handle large files in VMD I am always
> happy to know about it. (I saw Read Big DCD Files but I thought this
> way the calculations would be faster)
>
> Anyhow I will change my code from mol load to mol new just in case you
> will remove the load command. Maybe you should mention in
> http://www.ks.uiuc.edu/Research/vmd/current/ug/node138.html that load
> is deprecated.
>
> Thank you very much,
>
> Dipl.-Ing. Maximilian Ebert
>
> Etudiant au doctorat en biochimie
> Laboratoire du Dr. Joelle Pelletier
> Universite de Montreal
>
> m.ebert_at_umontreal.ca
>
> On 2013-02-26, at 5:16 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Max,
> At present there's not a way to silence the console output, but I
> wouldn't
> have expected you to get massive console output from just loading 20
> files.
> Are you loading each of the trajectories into a separate molecule
> for
> a particular reason? You should be using the newer "mol new" and
> "mol addfile"
> syntax when loading files, as the old "mol load" syntax is now
> deprecated
> and will be removed from the program eventually.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Feb 26, 2013 at 04:52:38PM -0500, Maximilian Ebert wrote:
>
> Hi list,
>
> I wrote a Tcl script to calculate the bfactor from a trajectory
> which was split into many pieces because the trajectory itself is
> too large to load as one file. It is working but now I want to
> execute it with less output. Since I load more than 20
> trajectories I don't want to see the output of:
>
> mol load psf $psffile dcd $item
>
> Is there a possibility to suppress it in the console? In addition,
> I wanted to know if someone knows why the Tcl console GUI is so
> slow compared to the console window? I am using Mac OS X 10.8.2
> and vmd 1.9.1.
>
> Thank you very much,
>
> Max
>
> --
> NIH Center 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
>
> --
> NIH Center 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 

-- 
NIH Center 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