VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Nov 16 2005 - 15:01:02 CST

Hi,
  DCD files cannot be concatenated with simple shell commands because
they contain a file header at the the beginning. You could conceivably
truncate the front end of the file using 'dd' or something, and then
concatenate them, but using 'catdcd' is the right way to do this.
At present VMD doesn't provide a means to append frames to existing
trajectory files, it can only create new files from scratch from the
trajectory timesteps that are resident in memory, so for your purposes
'catdcd' is the right tool for the job.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Nov 16, 2005 at 12:42:36PM -0700, Chang, Christopher wrote:
> Nuno,
>
> Do you know if cat'ing DCD files will work like this? If not, I could
> call Justin Gullingsrud's catdcd utility just as well, I guess. Thanks
> for the suggestion!
>
> Best,
>
> Chris
>
>
> _____
>
> From: Nuno R. L. Ferreira [mailto:nunolf_at_ci.uc.pt]
> Sent: Wednesday, November 16, 2005 12:36 PM
> To: Chang, Christopher
> Subject: Re: vmd-l: Appending to DCD file with "animate write"
>
>
> What about
>
> animate write dcd tmp.dcd beg $a end $a waitfor all sel
> $selection top
> cat tmp.dcd >> outname.dcd
>
> inside a loop?
>
> N.
>
>
> ----- Original Message -----
> From: Chang, Christopher
> <mailto:Christopher_Chang_at_nrel.gov>
> To: vmd-l_at_ks.uiuc.edu
> Sent: Wednesday, November 16, 2005 7:11 PM
> Subject: vmd-l: Appending to DCD file with "animate
> write"
>
>
> Hi,
>
> I am extracting an atom selection from very large DCD
> files, and would like to script something that will use a loop to read a
> frame, then append the atomselection to a new DCD file to lower memory
> demands. Can "animate write" do this? Right now the command
>
> animate write dcd outname.dcd beg $a end $a waitfor all
> sel $selection top
>
> in the loop with counter "a" and atomselection
> "$selection" overwrites each (a-1)th structure with the (a)th one.
>
> Thanks,
>
> Chris
>
>
>
> _____
>
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>
>
>
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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