From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu May 12 2011 - 01:53:23 CDT
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.
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
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,
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/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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