From: Viswanath Pasumarthi (
Date: Mon Sep 08 2014 - 14:05:10 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
I used 64-bit Windows 7 operating system, NAMD_2.9_Win32-multicore, NTFS
file system to store DCD file. Also, 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 suspect it would
be not possible to read the file anymore.

> 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.