VMD-L Mailing List

From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Thu Jan 15 2009 - 13:27:14 CST

Dear Axel,

> 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..
Do you have any script file that I can follow as an example on how to
store/restore data from/to user data fields in an efficient way?
Cheers
Cesar

Axel Kohlmeyer escribió:
> 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>
> 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>
> CLA> I would like to know
> CLA>
> 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...
>
> cheers,
> axel.
>
> CLA>
> CLA> Best regards
> CLA> Cesar Avila
> CLA>
>
>