VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Sep 20 2012 - 17:08:11 CDT

Hi,
  I don't recall if anyone replied to this, and I was out sick for a
few days after your email, but it is easy to write a .js file from
a given PSF/PDB pair by making an "all" atom selection and doing:
  $sel writejs filename.js

If your structure gets too large for psfgen to handle, you'll either
need to use the standalone version of psfgen that can write js files
directly, or I can make a special build of VMD for you that includes
a psfgen plugin that knows how to work with the js files. Eventually
this will be the standard version of psfgen shipped with VMD, but
I can't switch over to it until we get a few issues resolved for the
Windows version of VMD/psfgen.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Sep 07, 2012 at 09:57:39AM -0500, Ganesh Kamath wrote:
> Hi Folks,
> I have a system of polymer in water comprising around 440 A3 box or
> equivalent to ~8-9 million atoms.
> For memory reduction on the master node, I was told to generate a .js file
> instead of psf file.
>
> http://www.ks.uiuc.edu/Research/namd/wiki/?NamdMemoryReduction
>
> If using a js file, add the "usePluginIO yes" field and change your
> filename accordingly.
>
> Can someone please help me out. How do I use this plugin?
>
> thanks for your time.
>
> ganesh 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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