VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sun Nov 05 2006 - 07:47:42 CST

Hi Per,
you may want to look at using catdcd, which can isolate certain frames
and atoms, and then loading the stripped dcd into vmd or whatever else
you need to use. To strip atoms out with catdcd, run it with
-i indexfile
where indexfile contains a space-delimited list of the indices of atoms
you want to keep (usually, everything but water). If you load a psf/pdb
of your system of interest into VMD, you could write a suitable
indexfile by doing

set sel [atomselect top "not water"]
set ofile [open mypdb.ind w]
puts $ofile [$sel get index]
$sel writepdb stripped.pdb
close $ofile
$sel delete

You could then run, say,
catdcd -o stripped.dcd -i mypdb.ind inputdcd.dcd
to remove all waters and write the result to stripped.dcd.
You also need to write a new psf or pdb file containing only the atoms
you want included.

Best,
Peter

On Sun, Nov 05, 2006 at 12:56:34PM +0100, Per Jr. Greisen wrote:
> Hey all,
>
> Due to the size of my dcd-file I need to use the bigdcd to operate on my
> dcd-file. Normally I used a python-script to get the wanted coordinates
> from the simulation but I cannot use this here. So is there any tcl-script
> or a very simple template for getting out the coordinates where one is
> limited by bigdcd?
>
> Is it possible to limit the size by removing the water and how to do this?
> In the psf?
>
> Thanks in advance
>
> Best Regards
>
> Per Jr. Greisen
>