From: Viswanath Pasumarthi (v.pasumarthi_at_iitg.ernet.in)
Date: Mon Sep 08 2014 - 09:38:31 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.
Vega ZZ gives Code 44: Out of Memory & Code 483: Unknown or incompatible
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
No, I have not dealt with trajectory files larger than 4 GB before.
>
> 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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