VMD-L Mailing List

From: Jonathan Phillips (pcxjp3_at_nottingham.ac.uk)
Date: Tue Jun 25 2013 - 15:09:53 CDT

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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