VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jan 25 2008 - 14:32:42 CST

Irene,
  I'm assuming your running the machine out of memory. The easy
solution is to load chunks of the trajectory at a time as they will
fit into physical memory. You can either do this by writing another
loop that processes N frames at a time loading/deleting as necessary,
or you could use a variation of the BigDCD script and just have it use
the one-and-only frame that's loaded at each callback. Look in the
previous VMD-L messages last month or two for a few others that were
doing this.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jan 25, 2008 at 10:14:53AM -1000, Irene Newhouse wrote:
>
> Thanks to John Stone's help, I got my batch angle measuring script working. It now looks like this:
>
> mol load pdb tcnw.pdb dcd h5cnw.dcd
> set outf [open h5ctheta.txt w]
> set sel [atomselect top all]
> set nf [molinfo top get numframes]
> for {set i 0} {$i < $nf} {incr i} {
> set ang [ measure angle {22548 22527 22500} frame $i]
> puts $outf "$i $ang"
> }
> close $outf
>
> where the atom numbers were identified from tcnw.pdb.
>
> I invoke it like this:
>
> /share/apps/vmd_1.8.6/vmd -dispdev text -eofexit thet1.log
>
> My full dcd file contains 37429 frames & 1470 residues. This script works great with a test dcd I made by using catdcd to write every 10th frame, and it only takes 1 to 2 minutes to execute.
>
> I had left the full problem to run overnight & this morning it was still going - seemed to be hung up, so I put it out of its misery. I'm trying the full run again, having convinced myself the script ought to work, & it looks like it's hanging again. Am I
> running up against some allocation limit with the full dcd file?
>
> Thanks again!
> Irene Newhouse
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078