VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Tue Jun 25 2013 - 21:11:01 CDT

In my experience adding "waitfor all" makes dcd loading just as fast as
loading from the command line, as VMD won't pause and do a display
update inbetween frames. If you see individual frames being loaded, it
means the waitfor argument was not correctly set.
-Josh Vermaas

On 06/25/2013 05:09 PM, Thomas C. Bishop wrote:
> Thanks Jon,
> but my results seem to differ
>
> on the command line
> vmd -parm7 vac.parm -dcd dyn[1-5].nowat.dcd
> and
> vmd -dcd dyn[1-5].nowat.dcd -parm7 vac.parm
>
> give me same fast load behaviour and appear to be loaded before the
> full gui starts
>
> but when loading w/ a script as below vmd apparently
> loads the parm then reads the script, starts the full gui
> and then you can watch each frame as it loads.
>
> vmd -parm7 vac.parm -e ~/bin/load-anim.vmd -args dyn[1-5].nowat.dcd
>
> I tried
> update display off
> in my script but that did not help and animate vs mol add and even the
> waitfor off options.
> none of these beat loading the dcds on command line.
>
> FYI: I*'m using amber parm7 files and trajectories are dcd's
> calcualted w/ namd
>
>
> What am I missing?
>
> Tom
>
>
>
>
>
> On 06/25/2013 03:09 PM, 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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