VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jan 15 2009 - 10:34:56 CST

Cesar,
  You can download test versions of the next version of VMD
by following the instructions here:
  http://www.ks.uiuc.edu/Research/vmd/alpha/

The new test versions support multiple per-atom/per-timestep
user fields, so you can store things in "user", "user2", ..., "user4".

The DCD format doesn't have any provision for storing anything other
than coordinates or unit cell data. I haven't added support for
loading/saving the user fields in the new "js" format, but that
might be a possibility. You could also do a bit of scripting and either
write a binary file containing frames of user data yourself (Tcl has
ways of doing this efficiently) or you could write a text file, all
by scripting. I'll see about adding support for the "user" fields
in a future rev of the "jsplugin".

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jan 14, 2009 at 07:02:25PM -0200, Cesar Luis Avila wrote:
> Dear all,
> Regarding what I found on a previous message from Axel Kohlmeyer
>
> >data fields like mass, charge, beta, occupancy are stored
> >once per molecule. the only data fields that are once per
> >time step are x, y, z, and user. only the latest alpha test
> >versions add to this (e.g. multiple user files and velocities).
>
> I would like to know
>
> 1- Which is the alpha test version that he is referring to?
> 2- I think that also ufx, ufy and ufz are stored once per time step. Is
> there any problem on using these?
> 3- It would be very nice to be able to save this data in a file in such
> a way that it could be easily restored and loaded along with the dcd
> file. Is there such a feature in vmd?
>
> Best regards
> Cesar Avila 

-- 
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