Re: Unable to read corrupted binary DCD trajectory file

From: Gergely Gyimesi (
Date: Mon Sep 08 2014 - 09:51:33 CDT

Dear Viswanath,

It could also be because of a limitation of the file system you're using
to store the trajectory.


On 9/8/2014 16:04, 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.

Gergely Gyimesi, PhD
Postdoctoral Research Fellow
Institute of Biochemistry and Molecular Medicine
University of Bern
Bühlstrasse 28
CH-3012 Bern     | phone: +41 (0)31 631 4739
Switzerland      |

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