Re: DCD file really corrupt?

From: jonathan_at_ibt.unam.mx
Date: Wed Mar 29 2006 - 11:55:40 CST

Try opening it with a hexadecimal editor ("hexedit" in Linux), see if you can
read the title or, if you have some understanding of the format, try extracting
a few coordinates at the end by hand and see if they make sense.

Any way, I guess the best choice is to split the original file in the cluster
(or wherever the simulation was run) into less than 2GB pieces, and then
transfer them to your workstation.

J. Valencia

Quoting Lea Thgersen <lea_at_birc.au.dk>:

> Can it really be that I have lost everything because the file got larger
> than 2Gb???
>
> I cannot read in any way the DCD file from a 2ns simulation executed
> with the precompiled binary called NAMD_2.6b1_AIX-POWER-MPI on an IBM
> rs6000 pSeries 690 with AIX5.1D OS and tcl8.3.
>
> During the simulation I have frequently copied the dcd-file to my
> workstation (AMD64), used flipdcd, and studied the progress. However,
> since the size of the dcd-file got lager than 2Gb I haven't been able to
> open it in any way. Of course every time I copied the dcd-file to my
> workstation, the older version was overwritten (stupid, stupid me) so
> when the file suddenly gave me problems, I had no backup.
>
> When trying to use flipdcd on my workstation it gave the following:
> >flipdcd dmpc_sol2.eq.dcd
> dmpc_sol2.eq.dcd is not in DCD format
>
> I can understand it will give problems since I only have 2Gb memory on
> my workstation and flipdcd uses an amount of memory corresponding to the
> filesize (as far as I understand).
>
> When trying to use catdcd on my workstation it gave the following:
> >catdcd dmpc_sol2.eq.dcd
> CatDCD 4.0
> read_dcdheader returned -6
> Error: could not open file 'dmpc_sol2.eq.dcd' for reading.
>
> I guessed that maybe catdcd need it to be in native endian? Anyhow, I
> found some previous post on this list about problems with large dcd
> files from AIX:
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/3332.html
>
> Thereby inspired I got the latest cvs version of the plugin-tree for vmd
> and compiled a 64bit version of catdcd on the machine where the
> simulation was executed.
> However, whether I compile catdcd with gmake AIX5 or AIX5_64, I get the
> following output when trying to use it on my file:
>
> >catdcd dmpc_sol2.eq.dcd
> CatDCD 4.0
> dcdplugin) detected standard 32-bit DCD file of native endianness
> dcdplugin) read_dcdheader: corruption or unrecognized file structure
> Error: could not open file 'dmpc_sol2.eq.dcd' for reading.
>
> When trying to use flipdcd on the AIX machine I get the following
> >flipdcd dmpc_sol2.eq.dcd
> Can't stat dmpc_sol2.eq.dcd
>
>
> So again I ask you: Can it really be that I have lost everything because
> the file got larger than 2Gb???
>
> Thank you for any help
> Lea
>

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