VMD-L Mailing List

From: Ganesh Kamath (gkamath9173_at_gmail.com)
Date: Thu Sep 20 2012 - 17:25:29 CDT

Hi John,
  It took about 5-6 days for this system to build. The primary reason was
that I use patch to stitch the monomers of the polymer, the regenerate
angle and dihedral is memory intensive. Finally the water box of around 2
million molecules just took half a day.
Is there a parallel version of psfgen?
I am still making tests on the system.
Cheers,
Ganesh

On Sep 20, 2012 5:08 PM, "John Stone" <johns_at_ks.uiuc.edu> wrote:
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 syste... 

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