VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Mon Sep 08 2014 - 10:15:23 CDT

Hi Viswanath,

Just curious, but what operating system/NAMD build are you using? There
are some filesystems/NAMD builds that have hard upper limits on filesize
(FAT16 or 32-bit NAMD builds being possibilities that come to mind), and
weird things start happening when you exceed those limits. I don't know
very much about the internals of the dcd format, but can you at least
load the first frame? Or has the header been corrupted in some way that
VMD and other tools can't recover from? Basically we have no way of
knowing, and can't be very helpful with the information provided.

-Josh Vermaas

On 09/08/2014 09:03 AM, 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.
>
>
>
>