VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 11 2011 - 16:51:38 CDT

Hi,
  I think you're going to have to provide far more detail about
what exactly your script does. (e.g. with a copy of the script)
I had assumed that you might be making a common mistake, doing a
trajectory analysis (looping over frames), but that you might have
forgotten to use "waitfor all" on each of the "mol new" and "mol addfile"
lines when you first load your structure/trajectory data. If this
is not what you're doing, then you'll have to tell us much more
in order for anyone to help you.

Cheers,
  John

On Thu, Aug 11, 2011 at 05:42:32PM -0400, Sara baretller wrote:
> Hi John
>
> i made all my selections before i started the loop and then looped over
> the selections and update the selections
>
> so where should i add the waitfor all command ?? is it only useful when
> using animate ??
>
> I am not using animate but regular loop
>
> Thank you
>
> On Thu, Aug 11, 2011 at 5:36 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> When running your analysis on the supercomputer, did you make
> sure to use "waitfor all" when loading your files?
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
> On Thu, Aug 11, 2011 at 04:49:08PM -0400, Sara baretller wrote:
> > Hi all,
> >
> > i have a question about loading vmd to super computer , so my
> script works
> > fine in the local computer and i get data
> > but when i run th script in super computer i get simallar data to
> what i
> > got in local computer but after a certain number of frame, the
> data is
> > the same it looks like it does not load after the a certain frame ,
> i
> > tried loading from the that specific frames and still got same
> frozen data
> > ,
> >
> > does any body have any idea what is the problem thank you
> >
> > 9.64 32.33 20.49 32.83 10.43 4.46 28.78
> > 10.20 34.93 20.26 32.89 11.84 5.97 30.08
> > 9.96 35.54 19.75 32.66 11.95 6.48 29.27
> > 10.96 37.26 19.74 35.12 13.10 10.53 25.21
> > 12.39 40.20 22.51 35.56 13.37 9.37 29.11
> > 10.58 35.98 19.18 32.92 9.49 7.77 29.00
> > 11.87 37.69 19.44 32.70 10.60 7.94 28.34
> > 11.86 38.42 18.62 32.74 9.37 8.53 28.51
> > 12.30 36.45 18.08 34.30 10.28 8.76 29.13
> >
> > after here data frozen which does not happen when doing analysis in
> local
> > computer
> >
> > 12.30 36.45 18.08 34.30 10.28 8.76 29.13
> > 12.30 36.45 18.08 34.30 10.28 8.76 29.13
> > 12.30 36.45 18.08 34.30 10.28 8.76 29.13
> > 12.30 36.45 18.08 34.30 10.28 8.76 29.13
>
> --
> 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 

-- 
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