VMD-L Mailing List

From: Jeffrey Potoff (jpotoffx_at_gmail.com)
Date: Mon Nov 28 2011 - 15:00:35 CST

On 11/28/2011 12:45 PM, Axel Kohlmeyer wrote:
> On Mon, Nov 28, 2011 at 2:20 AM, Tessa Young
> <t.young5_at_student.unimelb.edu.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 

-- 
=================================================================
Jeffrey J. Potoff			  jpotoff_at_wayne.edu
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
http://potoff1.eng.wayne.edu
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