VMD-L Mailing List

From: Viswanadham Sridhara (muta.mestri_at_gmail.com)
Date: Tue Jul 25 2006 - 15:31:08 CDT

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.