VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jun 26 2013 - 09:26:04 CDT

Hi,
  If you're loading large trajectories and you want them to load
rapidly, you should add the "waitfor all" options to the load flags
so that VMD doesn't alternate between trajectory frame display
and loading. If you load files with "waitfor all" this allows VMD
to load them in their entirety at greater efficiency. Using the
waitfor all flag should also eliminate any differences one sees
that are the result of the order of file loading. When you loaded
your trajectory first, that was having the effect of not providing VMD
with structure info, making the display work "easier" and thus faster,
but that's still not as fast as skipping the display updates altogether
with waitfor all. If you use a script that loads files in a loop, you
would also want to use the waitfor all flags there as well:

foreach i $argv {
  puts "loading $i "
  mol addfile $i type {dcd} waitfor all
}

If this doesn't resolve the issue, then the next question is what version
of VMD you are running... :)

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jun 25, 2013 at 09:09:53PM +0100, Jonathan Phillips wrote:
> Hi Tom,
> I find that if I load my parameter file followed by my dcd, it's much slower then if I load my dcd followed by my parameter file.
> Don't know why, but getting rid of the '-parm7 vac.parm' bit and adding
>
> mol addfile vac.parm type {psf}
>
> to the end of the script may just do the trick.
> Jon Phillips
>
>
> ________________________________________
> From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Thomas C. Bishop [bishop_at_latech.edu]
> Sent: 25 June 2013 18:22
> To: vmd-l_at_ks.uiuc.edu
> Subject: vmd-l: load speed of dcds
>
> Dear VMD.
>
> I noticed a major difference in load speeds when reading dcds depending
> how I call load dcds (factor of 10ish)
>
> vmd -parm7 vac.parm dyn[1-5].nowat.dcd
> will load all five dcds (1000 frames each w/ 23,890atoms, 1.4G) nearly
> instantly
>
> vmd -parm7 vac.parm -dcd dyn1.nowat.dcd -dcd dyn2.nowat.dcd -dcd
> dyn3.nowat.dcd -dcd dyn4.nowat.dcd -dcd dyn5.nowat.dcd
>
> does the same
>
> BUT using a script that loops over the file names is very slow
> (comparatively)
>
>
> vmd -parm7 vac.parm -e ~/bin/load-dcds.vmd -args "dyn[1-5].nowat.dcd"
> takes a very long time (contents of load-dcd.vmd listed below)
>
> I've played w/ the "waitfor" option to the mol addfile
> and using animate read instead of mol addfile
> but still could not get same load speed as the initial command line.
>
>
>
> Any suggestions on how to improve read performance from w/in a "read
> file loop" would be GREATLY APPRECIATED.
>
> Thanks
> TOm
>
>
>
>
> **************************************
> more ~/bin/load-dcds.vmd
> foreach i $argv {
> puts "loadign $i "
> mol addfile $i type {dcd}
> }
>
>
>
>
>
>
> --
> *******************************
> Thomas C. Bishop
> Tel: 318-257-5209
> Fax: 318-257-3823
> www.latech.edu/~bishop
> ********************************
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-- 
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/