VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Sep 08 2014 - 10:00:13 CDT

Hi,
  What opearing system is your machine running? It sounds to me like
you are running NAMD on a machine that has a 4GB file size limit, perhaps
a very old version of Linux, Windows, or something similar? Another
possibility is that the filesystem is corrupt and that is why trying
to open the file even with fopen() yields an error. To give you further
assistance more information is needed from your side, about the
operating system(s) you're using, the filesystem that the DCD file is/was
being stored on, etc.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Sep 08, 2014 at 07:33:50PM +0530, Viswanath Pasumarthi wrote:
> Hi,
>
> I ran an NAMD simulation using 6 cores of an 8-cored, 8GB RAM, Intel-i7
> processor equipped PC. After running for 26 ns of simulation time, the
> size of the trajectory file has stopped increasing beyond 4 GB. The
> simulation is however finished by restarting from the last available
> coordinates. Now this 4GB DCD trajectory file is not being able to be read
> either using VMD or readdcd matlab file. While the VMD says, 'Unable to
> load molecule', fopen function (to read binary files) used in the readdcd
> matlab file returns fileID as -1, i.e. not able to open the input binary
> file.
>
> What is the cause the file size of the DCD stopped at 4 GB, despite having
> 8 GB RAM memory, and how can I now read this corrupted DCD trajectory
> file?
>
> Thank you,
> Viswanath.
>
>
> 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
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