From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Tue Aug 08 2006 - 17:08:50 CDT
Sorry... I was assuming you were using tcl (VMD) for doing this... This
would work:
animate write dcd truncated.dcd beg 0 end 20000 waitfor all sel $sel
~Neela
On 8/8/06, Jerome Henin <jhenin_at_vitae.cmm.upenn.edu> wrote:
>
> Dear Nar,
> The DCD format imposes that all frames have the same number of atoms. So
> the
> only way I see would be to have a VMD script that does the selection,
> updates
> it for each frame and saves coordinates to separate per-frame files.
> Binary
> files (like namdbin) would use much less disk space than PDB or similar
> text-based formats.
> Jerome
>
> On Tuesday 08 August 2006 15:04, Narender Singh Maan wrote:
> > Dear All,
> > I have a trajectory file for my simulation of a protein in a big water
> box.
> > Now to reduce the size i can extract and writeout the trajectory for
> 'just
> > the protein' from this system by using "catdcd" but my aim is to extract
> > some waters also (only those water molecules which are within 3.5 Ang.
> of
> > the protein surface...for each frame).Any suggestions would be of great
> > help.
> > thanks
> > Nar
>
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