From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Nov 11 2009 - 09:20:20 CST

Hi,
  You're likely running VMD out of memory by loading the whole 1.9GB DCD on
your system. What happens if you only load half of it? Another option
would be for you to make use of the "bigdcd" script and process it one
frame at a time.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Nov 11, 2009 at 04:04:34PM +0100, Gustavo Gust wrote:
> Dear colleagues,
> with vmd, I'm trying to use a script like this (vmd -dispdev text -e
> script.tcl), which select the O atoms from TIP3 water molecules at 3
> angstroms from the molecule GOL:
> package require pbctools
> set dir1 "/home/molecule/eq1"
> mol load psf $dir1/structure/file.psf dcd $dir1/file.dcd
> set nf [molinfo top get numframes]
> pbc readxst $dir1/file.xst -all
> pbc wrap -all
> pbc box
> set outfile [open file.dat w]
> for { set i 1 } { $i < $nf } { incr i } {
> set sel [atomselect top "(resname TIP3 and name OH2) and pbwithin 3 of
> (resname GOL)" frame $i]
> set nw [$sel num]
> puts $outfile "$i $nw"
> $sel delete
> }
> close $outfile
> Sometimes it's working fine, but frequently I get the following error
> message:
> terminate called after throwing an instance of 'std::bad_alloc'
> what(): std::bad_alloc
> Abort
> I'm using VMD 1.8.7 and, according to former messages in the mail list
> (Arneh Babakhani, Josh Stone, Feb 02 2007), I've included the line
> $sel delete
> but I couldn't fix this error. Also, I've tried to select index, but it's
> not working anyway.
>
> Is there other alternatives or suggestions to avoid this problem?
> I'm running VMD 1.8.7 in a Linux machine with Open Suse 10.3 and 2 Gb of
> RAM. Every dcd file has 1.9 Gb. The dimensions of the box are in xst
> file.
> Thank you for your attention,
> Gustavo Velardez

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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