VMD-L Mailing List

From: Justin Gullingsrud (justin_at_ks.uiuc.edu)
Date: Tue May 14 2002 - 10:03:16 CDT

Hi,

Check out CatDCD: http://www.ks.uiuc.edu/Development/MDTools/catdcd/

This program can create a new DCD file with just the atoms in a selection.
Let me know if you have any problems with it.

Cheers,

Justin

On Tue, May 14, 2002 at 10:51:06AM -0400, Storr, Mark wrote:
> Hi,
>
> with the following VMD provided script it is possible to make a particular
> selection and for each frame of an animation dump out that selection to
> separate pdb file.
>
> set sel [atomselect top "criteria"]
> set n [molinfo top get numframes]
> for { set i 0 } { $i < $n } { incr i } {
> $sel frame $i
> $sel update
> $sel writepdb water_$i.pdb
> }
>
> Obviously if one has a file with a large number of frames then this approach
> is somewhat prohibitive, one could change the incr i to only pick out
> certain frames, but the most obvious approach would be to write a new single
> dcd file which contains only the selected atoms at each frame. So I was
> therefore wondering if this is possible and if so how this may be achieved.
> Many Thanks
>
> Mark
> 

-- 
Justin Gullingsrud      3111 Beckman Institute
H: (217) 384-4220       I got a million ideas that I ain't even rocked yet...
W: (217) 244-8946       -- Mike D