Format of Binary Restart and Output Coordinate and Velocity Files

From: Joshua D. Moore (
Date: Fri Apr 18 2008 - 19:34:20 CDT


I just sent another message about Fortran and these files, but I really
would just like to know what is the format of these files. There is
somewhat of a description for the DCD files available from the website, but
nothing (as well as on the list) to describe in "words" the format of the
binary restart and output files.

It seems from the Output.C file that the subroutine write_binary does this
in a continuous stream with fwrite in C:

Number of atoms (int32)
X(i),Y(i),Z(i) (i = 1, Number of Atoms) (double precision, real*8 in

(Same for velocities after going through the scaling factor stuff....I
realize there is a factor of 20....something to get the velocities in
Angstrom/ps for the velocities)

However, despite the fact I can't read the entire file in fortran I don't
see the integer for the number of atoms at the beginning of the file and I
see the correct values starting from just the coordinates or velocities.

Is there some location that gives a better description of this format? In
the end I will probably write the code in C using fwrite as this format is
difficult in Fortran but it still doesn't solve the problem of understanding
what is the exact format.

Thanks for the advice.

Joshua Moore
Joshua D. Moore
Graduate Student
North Carolina State University
Dept. of Chemical and Biomolecular Engineering
Box 7905 Centennial Campus
Engineering Building I
911 Partners Way
Raleigh, NC 27695-7905
Phone: (919) 513-2051
Fax: (919) 513-2470

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