VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 25 2006 - 15:59:58 CDT

Hi,
  Yes, there's a DLPOLY plugin for VMD. There was a bug in the version
for VMD 1.8.4, which has been fixed, so you may want to try out one
of the test versions of VMD 1.8.5 until the final release is out:
  http://www.ks.uiuc.edu/Research/vmd/alpha/

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jul 25, 2006 at 04:31:08PM -0400, Viswanadham Sridhara wrote:
> Hi Everyone,
> Does VMD support to visualize output files obtained from DL_POLY ?
> Sorry that I did not do a good survey about this before putting this
> question in.
> Thanks in advance,
> -Vishy
>
>
> On 7/25/06, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> >
> >Jonathan,
> >Rather than writing your own trajectory writing code from scratch,
> >I'd suggest just using the VMD plugin interface to do this for you.
> >It's open source (UIUC Open Source License) and you can just put it into
> >your program as you wish. You could then read the code for CatDCD which
> >does (in part) exactly what you have in mind, and interface your code to
> >the plugin interface. This would allow your code to write output in any
> >of the trajectory formats that we have plugins for (that implement write
> >functionality):
> >http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/
> >
> >Let me know if you need more help.
> >
> >John Stone
> >vmd_at_ks.uiuc.edu
> >
> >On Tue, Jul 25, 2006 at 01:31:00PM -0400, Jonathan Ashar wrote:
> >> hello VMD,
> >>
> >> i am writing a molecular dynamics code as part of some undergraduate
> >research. i'd love to be able to use VMD to visualize my results. as such,
> >i'm trying to figure out the format of trajectory files. i'm willing to
> >use
> >the .dcd or .crd format, or any other format (AMBER, LAMMPS, etc.) -
> >whatever is easiest to code.
> >>
> >> i have found this
> >http://www.lrz-muenchen.de/~heller/ego/manual/node93.html description of
> >the .dcd/.crd format, but i dont think i could construct a complete .dcd
> >file from it (perhaps b/c i have no background in fortran). for example,
> >i'm
> >not sure what "i=1" means, or how to differentiate between different
> >timesteps.
> >>
> >> are there any more explicit, thorough descriptions of this or any
> >format?
> >> and as always, an example could be worth a hundred explanations :-P
> >>
> >> many thanks,
> >> jonathan ashar
> >--
> >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
> >
>
>
>
> --
> Viswanadham Sridhara,
> Graduate Research Assistant,
> Old Dominion University,
> Norfolk, VA-23529. 

-- 
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