From: Olaf Lenz (
Date: Thu Jul 16 2009 - 01:14:37 CDT

Hash: SHA1


First, let me point out that I have never used NAMD before, so I don't
know about the file types associated to it. The code for "pbc get -namd"
is code that was written by Jan Saam. I usually think in terms of the
VMD unitcell definition (a b c alpha beta gamma) instead of the cell
vectors. Jan is reading this list, I suppose, but I'll send an extra
copy to him anyway.

Indeed, John's suggestions is useful: would you mind sending me the .xst
and the trajectory files that you are talking about? It would very much
help to see what's the problem.

Patrick Kiley wrote:
>> Main< (xyz) 43 % pbc box -center com
> The problem I have is that the box I see is wrong (see attached)- it is not
> the box in my .conf file, .xst file, or the box in the beginning of my namd
> log file. All three of these agree. See below.

How did VMD learn about the unitcell geometry? Was the box size
contained in the trajectory file, or did you load it from the .xst file
via pbc readxst?

In any case, it looks as though the first base vector returned by
pbctools is aligned with the x-axis, while the NAMD output is not.
Indeed, VMD needs the first base vector aligned with the x-axis, so when
reading in an xst file via readxst, the system is automatically rotated
accordingly. If you then ask VMD to return the base vectors in NAMD
style, it will return the base vectors of the rotated system, not the
original ones. I believe that this explains the differences of the outputs.

> I couldn't find a similar problem anywhere in the docs/internet, so here
> are my questions: A) which is correct - I am inclined to believe what I see
> more than what I read, but then why is the .xst file in disagreement?

Is the picture really what came out when you used "pbc box -center com"?
Because it looks as though the box has its origin at the COM, not its

Otherwise, it is hard to see any error from looking at an image. I can
not say whether the box is correct. Do you see any inconsistencies with
what you expect from the behaviour of the system, or are you really just
worried about the numbers?

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