VMD-L Mailing List

From: Jonathan Phillips (pcxjp3_at_nottingham.ac.uk)
Date: Wed Jun 26 2013 - 06:45:28 CDT

I'm not sure you've tried what I meant or not, so I'll say it in long.
I find that these sorts of commands are fast:

vmd -parm7 vac.parm -dcd dyn1.nowat.dcd

vmd -dcd dyn1.nowat.dcd -parm7 vac.parm

vmd
followed by the vmd commands
mol addfile dyn1.nowat.dcd type {dcd}
mol addfile vac.parm type {parm7}

but that these are slow:

vmd
followed by the vmd commands
mol addfile vac.parm type {parm7}
mol addfile dyn1.nowat.dcd type {dcd}

and vmd -parm7 vac.parm
followed by the vmd command
mol addfile dyn1.nowat.dcd type {dcd}

So your vmd script comes in the slow category, but when you load from the command line I'd expect it to be fast.
If that doesn't solve your problem then I'm afraid I don't know.
Jon Phillips

________________________________________
From: Thomas C. Bishop [bishop_at_latech.edu]
Sent: 25 June 2013 23:09
To: Jonathan Phillips
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: load speed of dcds

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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may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.