VMD-L Mailing List

From: Pablo M. De Biase (pablodebiase_at_gmail.com)
Date: Mon Nov 28 2011 - 10:39:55 CST

The complete information of the periodic vectors in dcd format is missing
so its impossible to restore it from the dcd. I had the same problem so
what I did is I modified NAMD so to get a different dcd format with the
full periodic vectors in it so then I created tools for converting and
managing this new dcd-like format. I can help you giving the routines I
modified in NAMD if you need them.

On Mon, Nov 28, 2011 at 12:20 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.
>
> Is it possible to write out the cell size at the beginning of each pdb
> frame in the trajectory, using catdcd?
>
> Many thanks,
>
> Tessa
> VMD user
>