Re: coordinates and cells

From: Andreas Förster (
Date: Thu Feb 18 2010 - 04:47:29 CST

Rogan is right. Thanks. The .dcd file does indeed contain the cell
dimensions for each frame. I wasn't aware of that.

The cell dimensions correspond to those in the .xst file, but are
different from what I get when combining the .xst file with the .dcd
trajectory in VMD. I'm now working with the dimension from the .dcd
trace so it doesn't matter to me, but I still find this potentially


On 17/02/2010 5:25, Rogan Carr wrote:
> Hi Andreas,
> Why are you reading in the .xst at all, if you have a .dcd file? The dcd
> format holds the cell size, so you shouldn't need to read the .xst file.
> I'm not sure what's going on with your .xst file. The first line in the
> xst is always the system size on startup, so it shouldn't correspond to
> your first dcd frame (but rather, the restart.xsc file or system size
> that you started with).
> Rogan

         Andreas Förster, Research Associate
         Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London

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