Re: vmd-l: is possible to remove the waterbox before running VMD

From: John Stone (
Date: Thu Mar 09 2006 - 10:39:27 CST

  If you have a Unix machine handy, you can use the CatDCD program to strip
away atoms you're not interested in seeing. Typically, you'd use atom
selections in VMD to generate an 'index' file that CatDCD can use to
select the atoms you want to keep. You'd also produce matching psf/pdb files
using the '$sel writeXXX' atom selection file writing feature in VMD.
Once you have matching PSF/PDB/DCD files, you could then load it all up
into VMD.

  John Stone
On Thu, Mar 09, 2006 at 08:34:02AM -0800, lily jin wrote:
> I need the waterbox to do simulation. But when I show the result in VMD, the waterbox is not necessary, which takes a lot of memory. Is it possible to do simulation with waterbox and remove it from the trajectory before displaying in VMD?
> Thanks!
> Lily
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