AW: Corrupt dcd files

From: Norman Geist (
Date: Thu May 12 2011 - 01:53:23 CDT

Hi Marc,

Another question, what kind of filesystem do you use to save your dcd and
outfiles while namd is running? Is it a nfs source or a local disk?

Let me know.

Best regards

Norman Geist.

-----Ursprüngliche Nachricht-----
Von: [] Im Auftrag
von Marc Baaden
Gesendet: Mittwoch, 11. Mai 2011 18:16
Betreff: namd-l: Corrupt dcd files


I have recently observed a weird behaviour with at least 4 NAMD simulations
I ran locally on my machine. They all ran to completion but produced corrupt

dcd files. Is this a known issue?

Is there any tool that allows to retrieve as much as possible from such
dcd files? I have seen hints at using a hex editor, but I thought maybe
someone has gone through the trouble of writing a tool to do the job..
. eg is there any magic number or something one can jump to to skip
the corrupt parts?

Thanks in advance,
  Marc Baaden

dcdplugin) detected standard 32-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
dcdplugin) Warning: DCD header claims 4000 frames, file size indicates there
are actually 3999 frames
Info) Using plugin dcd for coordinates from file
dcdplugin) read_dcdstep: corruption or unrecognized file structure
Info) Coordinate I/O rate 59 frames/sec, 17 MB/sec, 7.5 sec
Info) Finished with coordinate file /Volumes/apple/

 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris      -
 FAX: +33 15841 5026  -  Tel: +33 15841 5176  ou  +33 609 843217

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