AW: Corrupt dcd files

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu May 12 2011 - 01:51:56 CDT

Hi Marc,

I'm sorry, I didn't see that you already showed the issue in your post.
Maybe you could try to write a little script in scilab or matlab for
example, because there are functions to read binary files and the file
description of binary dcd is surely shown somewhere in the net. You could
also try to use the flipdcd binary which is shipped with namd, maybe the
tool is able to recognize such things, or you can use the source to change
it to your needs.

Best regards

Norman Geist.

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

Hi,

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
/Volumes/apple/bcl1.prod.1.dcd
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/bcl1.prod.1.dcd.

-- 
 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:baaden_at_smplinux.de      -      http://www.baaden.ibpc.fr
 FAX: +33 15841 5026  -  Tel: +33 15841 5176  ou  +33 609 843217

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