From: Pablo M. De Biase (
Date: Mon Nov 28 2011 - 16:11:36 CST

If you are using constant pressure the box vectors are changing all the
time because the volume is fluctuating. So the vectors you have in the xst
file is only useful for the first frame not for the rest. If you are trying
to replicate the box with the correct box vectors you'll have to do
something similar to what I did.

On Mon, Nov 28, 2011 at 2:00 PM, Jeffrey Potoff <> wrote:

> On 11/28/2011 12:45 PM, Axel Kohlmeyer wrote:
>> On Mon, Nov 28, 2011 at 2:20 AM, Tessa Young
>> <**au <>>
>> wrote:
>>> Dear fellow vmd users,
>>> I have been using catdcd (version 4.0b) to create pdb trajectory files
>>> from
>>> namd dcd trajectory files. I have run constant pressure simulations
>>> (using
>>> periodic boundary conditions) with a varying periodic cell size. However
>>> when I use catdcd, the periodic cell size is only written out for the
>>> first
>>> frame and not for the following frames in the trajectory. Hence I have
>>> lost
>>> the periodic boundary information in the pdb output.
>> you also lost a lot of precision of your coordinate information.
>> Is it possible to write out the cell size at the beginning of each pdb
>>> frame
>>> in the trajectory, using catdcd?
>> only if you write out individual .pdb files for each frame and then
>> concatenate them together, e.g. using "cat". the CRYST1 record
>> is not written in the molfile function that writes out the coordinates.
>> overall, writing out .pdb trajectories should be avoided as much
>> as possible due to the massive loss of coordinate detail.
> Apparently I missed the original post...if one is determined to generate a
> bunch of PDB files, then it should not be too much of a stretch to write a
> shell script that grabs the cell vector data from the XST file and merges
> it with each PDB file.
> Agree with Axel, though. One is almost always better off working
> directly with the DCD file.
> Regards,
> Jeff
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> Jeffrey J. Potoff
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