VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Apr 16 2006 - 17:06:07 CDT

Hi,
  Ahh, so the real issue is that you need to be able to generate DCD
files that can be read by X-PLOR... Well, that shouldn't be too hard
to accomplish with one of the current versions, though I'll have to
make a small modification to the DCD plugin in order for you to do this.
The main reason that the new versions don't write X-PLOR format DCD files
anymore is because of the overwhelming preponderance of simulations run using
periodic boundary conditions. The X-PLOR DCD format didn't have a means of
storing unit cell information per-timestep, but the Charmm format does, so
VMD writes DCD files in the Charmm format by default. Since I'd rather that
people use the current version of VMD than dig up old ancient ones, I've
made a small change to the VMD DCD plugin which will allow you to force
it to write DCD files in X-PLOR format, even though that will mean losing
unit cell info etc. In order to enable this output mode, you'd either do:
(before running VMD)
  setenv VMDDCDWRITEXPLORFORMAT 1

or (in the VMD Tcl console)
  set env(VMDDCDWRITEXPLORFORMAT) 1

This will be in the next build I do, or I can send you a DCD plugin you can
copy into one of the VMD 1.8.4 test versions if you like.

  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Apr 16, 2006 at 10:41:12PM +0300, danfishl_at_post.tau.ac.il wrote:
> I need this specific one because after my MD runs on NAMD at the biowulf
> cluster, I want to do covariance analysis using xplor but fot some reason it
> does not read NAMD dcd files so what I did until now is open the dcd file with
> VMD 1.8a21 and save it as a dcd with the same name (overwrite it) and then all
> my dcd file whould be read by xplor. Other version dont work this way
> (strange...)
> I need this version locally on my computer for faster saving of the dcd files
> which are heavy.
> Thanks a lot, Dan.
> P.S. Have anyone ask you for such a bizzar request.
>
>
>
> Quoting John Stone <johns_at_ks.uiuc.edu>:
>
> >
> > Hi,
> > The old test versions (1.8 is quite old, and 1.8a21 is _really old_)
> > aren't available on the download page anymore. If you really need that
> > specific version for some reason, tell me why and I will see if I've got
> > a copy of that test version backed up somewhere. You'd be much better
> > served to run one of the current versions however.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Sun, Apr 16, 2006 at 06:02:34PM +0300, Dan Fishelovitch wrote:
> > > Hi.
> > > I wanted to download VMD version 1.8a21 but its not in the VMD download
> > list.
> > > Can it be downloaded somehow?
> > >
> > > Thanks, Dan.
> > --
> > 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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> > at the Tel-Aviv University CC.
> >
>
>
>
>
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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