VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Nov 28 2011 - 11:45:47 CST

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.

cheers,
   axel.

>
> Many thanks,
>
> Tessa
> VMD user
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.