VMD-L Mailing List

From: Chris Harrison (charris5_at_gmail.com)
Date: Thu Sep 20 2012 - 18:25:22 CDT

Ganesh,

Not yet.

Chris

Ganesh Kamath <gkamath9173_at_gmail.com> writes:
> Date: Thu, 20 Sep 2012 17:25:29 -0500
> From: Ganesh Kamath <gkamath9173_at_gmail.com>
> To: John Stone <johns_at_ks.uiuc.edu>, vmd-l_at_ks.uiuc.edu, Ganesh Kamath
> <gkamath9173_at_gmail.com>
> Subject: Re: vmd-l: Question about generating a .js file
>
> 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...
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078

Best,
Chris 

--
Chris Harrison, Ph.D.
NIH Center for Macromolecular Modeling and Bioinformatics
Theoretical and Computational Biophysics Group
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
http://www.ks.uiuc.edu/Research/namd       Voice: 773-570-6078
http://www.ks.uiuc.edu/~char               Fax:   217-244-6078