Re: Read DCD file in Java

From: Axel Kohlmeyer (
Date: Sat Jun 06 2009 - 11:23:50 CDT

On Sat, 2009-06-06 at 13:39 +0800, Kejun (Kevin) Dong wrote:
> Hi All,
> I want to stream the dcd data from one server to another by frames and
> it is the first step to parse the dcd files in Java.
> Does anyone have the source code to read dcd files in Java?


i don't have any java code, but i can give you some
unsolicited advice. parsing .dcd files cleanly and
reliably is a painful exercise. dcd is fortran unformatted
binary output. as such the exact number and order of bytes
in it changes due to endianness and other characteristics
of the machine or the compiler (and compiler flags) that
were used when compiling the original code.

the VMD molfile library contains a plugin that can handle
a very large variety of these different incarnations of
dcd files. it is written in c, so you can consider either
interfacing or translating it to your code.


> I would really appreciate your help!
> -Kevin Dong

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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