VMD-L Mailing List

From: Irene Newhouse (einew_at_hotmail.com)
Date: Fri Jan 25 2008 - 14:56:47 CST

Thanks so much. I'll do that when I have time. I discovered by trial & error that every 5th frame still works & for what I want right now, that's good enough.
 
Irene> Date: Fri, 25 Jan 2008 14:32:42 -0600> From: johns_at_ks.uiuc.edu> To: einew_at_hotmail.com> CC: vmd-l_at_ks.uiuc.edu> Subject: Re: vmd-l: re: script hangs when use full dcd file> > > 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> > _________________________________________________________________> > Need to know the score, the latest news, or you need your Hotmail®-get your "fix".> > http://www.msnmobilefix.com/Default.aspx> > -- > 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
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