From: Axel Kohlmeyer (
Date: Wed Jan 14 2009 - 14:56:10 CST

On Wed, 14 Jan 2009, Cesar Luis Avila wrote:

CLA> Dear all,

dear cesar,

CLA> Regarding what I found on a previous message from Axel Kohlmeyer
CLA> >data fields like mass, charge, beta, occupancy are stored
CLA> >once per molecule. the only data fields that are once per
CLA> >time step are x, y, z, and user. only the latest alpha test
CLA> >versions add to this (e.g. multiple user files and velocities).
CLA> I would like to know
CLA> 1- Which is the alpha test version that he is referring to?

the ones in the regular places. multiple user fields were added
quite a while ago, but then again, it has been quite a while since
the last release. i'm usually working with my self-compiled versions
of VMD which are built from the (readonly) cvs version, so i always
have to look up the changelog file to check at what point something
was available. so multiple user fields were added on 2007-10-03, for
example, so after the 1.8.6 release (which was 2007-04-07).

CLA> 2- I think that also ufx, ufy and ufz are stored once per time step.
CLA> Is there any problem on using these?

those were itended for IMD, but i don't think that
there would be a big problem.

CLA> 3- It would be very nice to be able to save this data in a file in such a
CLA> way that it could be easily restored and loaded along with the dcd file.

...or a new file format that contains all data in a consistent way,
so you don't have to shuffle multiple files around and make certain
that they are consistent.

CLA> Is there such a feature in vmd?

not really. well, not yet, that is.
feel free to pick up your favorite text editor and help implementing it.

you can of course write a script that stores the information in some
(flat format) text file and then load this back with another script.
this is what i am doing, since most of the properties that i compute
and store in the user fields take a lot of time to compute...


CLA> Best regards
CLA> Cesar Avila

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.