From: Michael Kreim (mkreim_at_keychem.de)
Date: Sat May 30 2009 - 07:12:34 CDT

Dear NAMD users,

I have some problems with my DCD trajectory files.

I am running NAMD 2.6 on 32 nodes of my university's parallel computer.
 The system consists of 14 SMP-nodes (Typ IBM 9125-F2A p575) with 448
Power6-CPUs, connected using Infiniband and GBit-Ethernet. The
operating system is AIX.

Because of some limitations in the IBM queuing system NAMD runs for 24
hours, resubmits the job and restarts from the previous run.

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.

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.

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,



The beginning of the NAMD-logfile

$ cat 02_md.4.namd.log
Info: NAMD 2.6 for AIX-POWER-MPI
Info: Based on Charm++/Converse 50900 for mpi-sp
Info: Built Fri Mar 14 10:25:57 MET 2008 by mkreim on hlr0a
Info: 1 NAMD 2.6 AIX-POWER-MPI 32 hlr5f mkreim
Info: Running on 32 processors.
Info: 116736 kB of memory in use.
Info: Memory usage based on sbrk
Info: Changed directory to .
Info: Configuration file is 02_md.namd
TCL: Suspending until startup complete.
Info: EXTENDED SYSTEM FILE ./results/02_md.xsc

VMDs output while reading such a DCD file
$ vmd -dispdev text 02_md_start.psf 02_md.4.dcd
Info) VMD for LINUXAMD64, version 1.8.6 (April 6, 2007)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 4 CPUs detected.
Info) Free system memory: 10429MB (64%)
Info) File loading in progress, please wait.
Info) Using plugin psf for structure file ../../data/02_md_start.psf
Info) Analyzing structure ...
Info) Atoms: 20483
Info) Bonds: 13638
Info) Residues: 6845
Info) Waters: 6819
Info) Segments: 3
Info) Fragments: 6845 Protein: 0 Nucleic: 0
dcdplugin) detected standard 32-bit DCD file of opposite endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
Info) Using plugin dcd for coordinates from file 02_md.4.dcd
Info) Finished with coordinate file 02_md.4.dcd.

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