dcd binary file format

From: Jianhui Tian (jianhuitian_at_gmail.com)
Date: Tue May 01 2007 - 14:41:53 CDT

*Hi all,*
*I am writting my own fortran code to read the dcd file written by NAMD 2.6. I
am not sure what the binary file are writting there and it's impossible to
guess. I find one description about the format(what are written there) at:*

The format of the binary trajectory (DCD) file is illustrated in the
following example:

   - For the first coordinate set:

HDR,ICNTRL ! character*4 HDR, integer
NATOM ! integer NATOM

   - If fixed atoms exist (for example, NFREAT.NE.NATOM), an extra record
   exists with the list of free (movable) atoms:


   - If this is crystal-type calculation (for example, a constant
   pressure job), an extra record exists with unit cell parameters in
   lower-triangle form:

(X(I),I=1,NATOM) ! real X(NATOM)
(Y(I),I=1,NATOM) ! real Y(NATOM)
(Z(I),I=1,NATOM) ! real Z(NATOM)

 For all subsequent coordinate sets, only movable atoms are written.

   - If this is a crystal-type calculation (such as a constant pressure
   job), an extra record exists with unit cell parameters in lower-triangle


 Where HDR = `CORD' or `VELD' for coordinates and velocities, respectively:

ICNTRL(1)=NFILE ! number of frames in trajectory file
ICNTRL(2)=NPRIV ! number of steps in previous run
ICNTRL(3)=NSAVC ! frequency of saving
ICNTRL(4)=NSTEP ! total number of steps
ICNTRL(8)=NDEGF ! number of degrees of freedom
ICNTRL(9)=NATOM-NFREAT ! number of fixed atoms
ICNTRL(10)=DELTA4 ! coded time step
ICNTRL(11)=stoi(XTLTYP,ALPHABET) ! coded crystallographic
! group (or zero)
ICNTRL(20)=VERNUM ! version number

 All other entries (12-19) are zero.

 *It seems that the new dcd file is not written out following this format.
(You can see, the format here writes the whole file "in many lines".
**Instead, my
dcd file here writes everything in "one single line", which means you can
only use "read(unit)" once.)* *Could anyone please clarify for me and tell
me what are writting sequentially in the binary file? Thanks a lot. *


This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:37 CST