Unable to read corrupted binary DCD trajectory file

From: Viswanath Pasumarthi (v.pasumarthi_at_iitg.ernet.in)
Date: Mon Sep 08 2014 - 09:04:32 CDT


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

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

Thank you,

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