VMD-L Mailing List

From: Olaf Lenz (olenz_at_fias.uni-frankfurt.de)
Date: Thu Feb 14 2008 - 16:05:32 CST

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Hi!

Thomas C. Bishop wrote:
| 1) do the periodic images displayed with (graphics reps -> periodic ->
| +x ; -x etc....) get the PBD dimensions updated every step when
| displaying an animation of the trajectory?

When you have loaded the periodic information, then yes. Not all formats
do actually save this information, but those that do work fine.

| Since there is an exwithin command... how about a pbcwithin command?

That would be a good thing. As far as I understood, the whole periodicty
issue is currently redesigned, so I think afterwards we will have
something comparable.

| 3) is there a way to easily display the periodic box size
| e.g. a "show pbcbox" or "get pbc dimensions" command or some other way
| to obtain values for the PBC dimensions within VMD if it has read them
| from the DCD

In fact, there is the "pbctools" plugin that can do all this and more:

        http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/

Best regards

        Olaf

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