Re: coordinates and cells

From: Rogan Carr (
Date: Wed Feb 17 2010 - 11:25:06 CST

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).


On Feb 17, 2010, at 11:00 AM, Andreas Förster wrote:

> Dear all,
> I'm trying to match box sizes with frames of a trajectory. I did a
> 60-ns nvt simulation that generated a dcd with 6000 frames and an
> xst with 6000 box dimensions. After reading the xst file into VMD
> using the PBCTools plugin, I find that the first frame of the
> trajectory has the second cell from the xst file associated with it
> (comparing output from 'pbc get' with xst file). The second to last
> frame is associated with the last cell from the xst file. The last
> frame seems orphaned, but cell dimensions are reported anyway.
> Those are nowhere in the xst file. That doesn't make sense to me.
> The first frame of the dcd was written at the same time as the first
> line of the xst. Now, it says that 'pbc readxst' skips the first
> line by default, but it still seems a rather strange effect.
> As a curious aside, my simulation starts at step 406,000 with
> coordinates written to the trajectory every 10,000 steps. In the
> namd log file, an early line reads 'DCD FIRST STEP 416000', as it
> should. However, coordinates are then written at 410000, 420000
> etc. Does that have something to do with the offset I observe?
> I'm asking because I'm trying to push my protein back into the water
> box for analysis, and I want to make sure I use the right cell with
> the right model - otherwise it's all bogus. For now I'm just
> looking at the coor and xsc files in the hope that they match.
> Thanks.
> Andreas
> I'm using NAMD 2.7 compiled from cvs on RHEL 5.4, 64-bit.
> --
> Andreas Förster, Research Associate
> Paul Freemont & Xiaodong Zhang Labs
> Department of Biochemistry, Imperial College London

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