From: Axel Kohlmeyer (
Date: Mon Nov 28 2011 - 17:13:02 CST

On Mon, Nov 28, 2011 at 5:11 PM, Pablo M. De Biase
<> wrote:
> 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.

no. periodic box replication is independent of the origin
and in NAMD/CHARMM it is guaranteed that the first
vector is always along the x-axis, the second in the
xy-plane and that you have a right-handed coordinate
system. thus information in the .dcd file is sufficient.

only if you want to allow arbitrary box vector orientations,
like they are used in condensed matter DFT calculations
(for efficiency reasons), then you have a problem with
this information. this is the reason why the molfile plugins
for gaussian cube files and .xsf files rotate the box (and
the enclosed coordinates and grids) to match the
conventions from above.

> 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
>>> <>  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
>> --
>> =================================================================
>> Jeffrey J. Potoff               
>> Associate Professor                       Wayne State University
>> Department of Chemical Engineering and Materials Science
>> 5050 Anthony Wayne Dr                     Phone:(313)577-9357
>> Detroit, MI 48202                    Fax:  (313)578-5815
>> =================================================================

Dr. Axel Kohlmeyer
College of Science and Technology
Temple University, Philadelphia PA, USA.