VMD-L Mailing List

From: Thomas C. Bishop (bishop_at_tulane.edu)
Date: Thu Sep 02 2010 - 14:28:55 CDT

Dear VMD,

For purposes of analysis I often break a DCD into pdbs that are written to disk, analyze them with another program and remove the pdbs.
Can I avoid writing them to disk by using named pipes or sockets.
I've considered a ram disk as another option.

To my surprise, I noticed that sometimes when I write a pdb, analyze it and remove it w/in a script
that there seems to be no actual disc activity. Every thing happens in buffers before anything is committed to disc.

Given this observation should I just let the OS handle things rather than force the issue w/ pipes/sockets?

What if any chances are there for data corruption if I pass data via pdbs in this manner.

Thanks
Tom
***************************

Example: once the initial DCD is loaded there is NO disc activity (well the HD light does not blink)
during the entire for loop.

vmd -psf some.psf -dcd some.dcd

then issue these commands

set skip 1
set numframes [molinfo top get numframes]
set all [atomselect top "all"]

for {set i 0} {$i < $numframes} {incr i $skip} {
    puts " working on $i "
    set outfp [format "%06d" $i ]
    $all frame $i
    $all writepdb tmp.pdb
    rm tmp.pdb
}

*******************************
   Thomas C. Bishop
    Tel: 504-862-3370
    Fax: 504-862-8392
http://dna.ccs.tulane.edu
********************************