Re: Unable to read corrupted binary DCD trajectory file

From: Kenno Vanommeslaeghe (
Date: Mon Sep 08 2014 - 16:38:48 CDT

On 09/08/2014 04:27 PM, Viswanath Pasumarthi wrote:
> I used 64-bit Windows 7 operating system, NAMD_2.9_Win32-multicore

Well there's the root source of your problem; addresses [within a file]
beyond 4GB cannot be expressed using 32 bits. The NAMD download site also
offers 64-bit Windows binaries, which would presumably not suffer from
this issue.

> Your fears have come true. From what I see from the readdcd run, the DCD
> header is corrupted as the NAMD tried to overwrite the DCD file once the
> file size reached the apparent limit of 4 GB (reason is still mystifying
> to me). The important information relating to endoffile, N (no. of atoms),
> timestep, DELTA etc. have been overwritten. I understand it would not be
> possible to read the file anymore.

"Not possible" is pretty absolute. It would hypothetically be possible to
recover a good chunk of data, just _very_ difficult, and quite possibly
not worth the effort. So, I'm truly sorry to hear you'll need to re-run
your simulation. Learning experiences are a good thing, but they needn't
be *this* painful :(

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