VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Feb 27 2013 - 10:34:02 CST

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
>
> Étudiant au doctorat en biochimie
> Laboratoire du Dr. Joelle Pelletier
> Université de Montréal
>
> 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