CatDCD is built using the molfile reader/writer plugins as the basis for it's file processing features, but is made available as a standalone program that can be compiled and run independently of VMD itself.

CatDCD is available for download from the MDTools page: http://www.ks.uiuc.edu/Development/MDTools/catdcd/

* catdcd *
* Written by Justin Gullingsrud, based on DCD I/O code from VMD

* FEATURES *
- catdcd functions much like the Unix "cat" command: it concatenates DCD files
into a single DCD file.  It also allows the user to specify which atoms and
which frames should be written into the output file; thus DCD's can be split
as well as combined.

* USAGE *
catdcd -o  [-i ] [-first first] [-last last]
               [-stride stride]   ...

OR

catdcd -num   ...

-o : Specify the output file for CatDCD.  Required, unless -num
is present (see below).

-num: When present, no output file will be written.  Instead, CatDCD prints
the number of frames in each file, then exits.
 
-i :
 should contain the (zero-based) indices of the atoms in the
dcd files whose coordinates are to appear in the output file.  The indices
should be ASCII text, separated by whitespace.

-first first: Specify the first frame to be written to the output file.  
Default is 1 (write starting from the first frame read).

-last last: Specify the last frame to write.  Default is the last frame in 
the last file.

-stride stride: Specify how many frames to skip when writing.  Default is 1
(don't skip any frames).


* CAVEATS *
The input files may be any combination of charmm or xplor format, and big-
or little-endianness.  However, they must all have the same number of atoms.

The code uses only standard C library commands and should thus be portable to 
pretty much anywhere, including non-Unix platforms (I haven't tested this ;-)
 
DCD's with fixed atoms will not work properly. (FIXED in version 3.0)

* EXAMPLES *

catdcd -num eq01.dcd eq02.dcd

	Prints the number of frames in the two DCD files, then the total,
	then exits.

catdcd -o eq_all.dcd eq01.dcd eq02.dcd eq03.dcd

	Combines eq01.dcd, eq02.dcd, and eq03.dcd into eq_all.dcd.

catdcd -o eq_pro.dcd -i protein.ind eq01.dcd 

	Takes only the coordinates corresponding to the indices in 
	'protein.ind' from eq01.dcd and writes them to eq_pro.dcd

catdcd -o eq_first.dcd -first 1000 -last 2000 -stride 10 eq01.dcd eq02.dcd
	
	After skipping 999 frames, writes the 1000 frame and every 10th
	subsequent frame to eq_first.dcd, until a total of 2000 frames 
	have been read.  	

* Installation * 
Unpack the distribution package.  A directory named catdcd will be created.
Enter that directory and type "make".  To use a different compiler or compile
flags, edit the first three definitions in the Makefile.

New in version 3.0:
  * Now uses the VMD plugins for file reading.  This makes it very easy
    to adapt the program to handle other file formats.
  * Use of VMD file readers means fixed atoms are handled automatically.
  
New in version 2.0:
	* New command line interface: The -o option is now required for 
	  setting the output file.
	* New -num option to print the number of frames in each file, as well
	  as the total.
	* Fixed a bug in the DCD reading code that caused misreading of the
	  DELTA parameter for byte-swapped Charmm DCD files; caused floating-
	  point exceptions on Alpha platforms.

New in Version 1.3:
	* Fixed free of uninitialized pointer when no -i option is set.
	* Fixed bug in reading of opposite-endian Charmm-format dcd files.

New in Version 1.2:
	* Fixed serious bug that appeared in 1.1; only frames from the first 
	  input file were being written to the output file.

New in Version 1.1:
	* Added -first, -last, and -stride flags.
	* Added version number information to the output.