VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jun 26 2013 - 11:45:46 CDT

Tom,
  The "waitfor 1" just tells VMD to wait until 1 frame has been loaded.
The "waitfor 0", tells it not to wait at all.
The "waitfor -1" is another way of saying "waitfor all".
Any number N >= 1 tells VMD to wait for that many (N) frames
to be loaded before going back to processing user inputs, scripts, etc...

Cheers,
  John

On Wed, Jun 26, 2013 at 11:19:15AM -0500, Thomas C. Bishop wrote:
> Thanks JOhn and thanks for the explanation.
> The documentation provides all the information I need.
>
> IN short... RTFM..
> "read the fresh manual" is not "read the first manual" :-)
>
>
> "waitfor all"
> works as advertised.
>
> IN some of my scripts I have
> "waitfor all" and some "waitfor 1"
>
> so where did "waitfor 1" come from in my scripts?
>
> The "waitfor 1" lines are in my scripts that I developed with the
> logfile option to VMD.
> which dumps
> mol addfile {dyn1.dcd} type {dcd} first 0 last -1 step 1 waitfor 1 0
> for default options
>
> clicking "load all at once" in the gui dumps
> mol addfile {dyn2.dcd} type {dcd} first 0 last -1 step 1 waitfor -1 0
>
> which gives the "fast load"
>
> There are good reasons to use waitfor 1 in some scripts.
> (can't recall any at the moment)
>
>
> I suspect that the "waitfor" options have changed since I wrote my
> first VMD script in circa 1996 :-). I think 1 or 0 used to mean "all"
> ....RTFM...
>
> Tom
>
>
>
> On 06/26/2013 09:26 AM, John Stone wrote:
> >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
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