coordinates and cells

From: Andreas Förster (
Date: Wed Feb 17 2010 - 11:00:54 CST

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.



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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