From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 09 2006 - 10:40:39 CST
Oops, I intended to provide the URL to the CatDCD page as well:
http://www.ks.uiuc.edu/Development/MDTools/catdcd/
John Stone
vmd_at_ks.uiuc.edu
On Thu, Mar 09, 2006 at 10:39:27AM -0600, John Stone wrote:
>
> Hi,
> 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
> vmd_at_ks.uiuc.edu
>
> 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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> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
-- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns_at_ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
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