VMD-L Mailing List

From: Izrailev, Sergei (Sergei.Izrailev_at_3dp.com)
Date: Tue Sep 30 2003 - 11:21:35 CDT

Hi,

(John, - I dug this up - is this a candidate for FAQ?)

There's a description of the X-PLOR variation of DCD format here
(http://www.lrz-muenchen.de/~heller/ego/manual/node93.html):

The DCD format is structured as follows (FORTRAN UNFORMATTED, with Fortran
data type descriptions):

HDR NSET ISTRT NSAVC 5-ZEROS NATOM-NFREAT DELTA 9-ZEROS
`CORD' #files step 1 step zeroes (zero) timestep (zeroes)
                        interval
C*4 INT INT INT 5INT INT DOUBLE 9INT
==========================================================================
NTITLE TITLE
INT (=2) C*MAXTITL
                (=32)
==========================================================================
NATOM
#atoms
INT
==========================================================================
X(I), I=1,NATOM (DOUBLE)
Y(I), I=1,NATOM
Z(I), I=1,NATOM
==========================================================================

and the following describes the difference between X-PLOR
and CHARMm formats:
(http://www.ocms.ox.ac.uk/mirrored/xplor/manual/htmlman/node230.html)

Binary Trajectory Files
The file format is identical to the CHARMm-DCD format (Brooks et al. 1983,
which can be read by QUANTA and a variety of other programs. The only
exception is that the number of coordinate sets written to the trajectory
file is explicitly written into the header of CHARMm-DCD files, whereas
XPLOR writes a zero instead.

I hope this helps...

Sergei

-----Original Message-----
From: John Stone [mailto:johns_at_ks.uiuc.edu]
Sent: Monday, September 29, 2003 11:53 AM
To: FUNG WAI KEUNG
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: File format of DCD Trajectory file

Hi,
  The only reference I ever had to work with was from a printed X-PLOR
manual as I recall, which I don't seem to have handy at this moment.
If you're curious, there are many programs out there that can read/write
DCD files, so probably the best thing would be to look at the code that
some program uses if you're unable to find an actual file format spec.
If you're thinking of writing out your own DCD trajectory files, you might
consider using XYZ or another simpler format instead. The DCD files
are binary, so you have things like machine word-size and endianism to
worry about.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Sep 29, 2003 at 02:10:13PM +0800, FUNG WAI KEUNG wrote:
> Dear VMD users,
>
> Would you please direct me to the information of the file format of DCD
> trajectory file?
>
> Thanks in advance.
>
> ========
> Regards,
> Wai-keung, Fung
>
> Department of Automation and Computer-Aided Engineering,
> The Chinese University of Hong Kong,
> Shatin, N.T.,
> Hong Kong
>
> Tel: (852)26098056 Fax: (852)26036002
> Email: wkfung_at_acae.cuhk.edu.hk 

-- 
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