Re: flipdcd

From: Axel Kohlmeyer (
Date: Mon Jun 01 2009 - 12:05:35 CDT

On Sat, 2009-05-30 at 14:12 +0200, Michael Kreim wrote:
> Dear NAMD users,
> I have some problems with my DCD trajectory files.


> My problem is, when I download the NAMD output files to my local linux
> computer and try to change the endianes using flipdcd I get for some,
> but not for all (!), of the files the following error message:
> $ ./flipdcd -s 02_md.4.dcd
> 02_md.4.dcd is not in DCD format.

have you tried using catdcd instead of flipdcd. the latter
will expect the trajectory in host endian order, which the
molfile plugins which catdcd uses should be able to handle
big endian trajectories regardless of endianness.

> I need to flip the endianes because I analyse the trajectories using a
> inhouse application that needs the files in little-endian. The parallel
> computer saves in big-endian.

in that case i would also strongly recommend to consider adding
an interface to the molfile library to this code to make transfer
of data more convenient.


> Do you know some reasons that could be the reason for this error? Do you
> have any ideas how to repair my dcd-files so I can flip them?
> I put some information from my namd log and the output from vmd reading
> such a dcd-file at the end of this mail. If you need some more
> information please tell me.
> Thanks in advance.
> With best regards,
> Michael
> P.S.:

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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