Re: Unable to read corrupted binary DCD trajectory file

From: Viswanath Pasumarthi (v.pasumarthi_at_iitg.ernet.in)
Date: Mon Sep 08 2014 - 09:43:47 CDT

> You wouldn't be running a 32-bit OS, would you? There, file size is
> limited to just beyond 4 GB.
No, this is a 64-bit Windows 7 operating system. Cross checked it.

>
>
> Andreas
>
>
>
> On 08/09/2014 3:04, 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.
>>
>>
>
> --
> Andreas Förster
> Crystallization and X-ray Facility Manager
> Centre for Structural Biology
> Imperial College London
>
>

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