From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Mon Sep 08 2014 - 09:13:35 CDT
Viswanath,
VegaZZ
(http://nova.disfarm.unimi.it/cms/index.php?Software_projects:VEGA_ZZ:Download)
most probably will be able to read your corrupted trajectory; save a
file in new trajectory file.
Did you have any files larger than 4 GB on computer where you run NAMD
simulation, also bad sectors on disk can causes problem
Branko
On 9/8/2014 4:04 PM, 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.
>
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