VMD-L Mailing List

From: Viswanath Pasumarthi (v.pasumarthi_at_iitg.ernet.in)
Date: Mon Sep 08 2014 - 10:01:07 CDT

> 8GB ram has nothing to do with the size of the file stopping at 4GB. The
> trajectory is written to your hard drive. You have restart files. Try
> restarting the simulation and see if it crashes at the same point. Usually
> the output is more informative. Try looking at the log file and paste the
I am afraid you misunderstood the problem. There is no 'error'. The DCD
file has stopped to increase in its file size after reaching 4 GB. I have
observed for few hours of run time, equivalent to few nanoseconds, to
understand that either the new coordinates are not being appended at the
end of the DCD file or the DCD file itself is being overwritten. This led
me to stop the simulation and restart from the last point.

> exact error. It could be that your hard disk is full and there is no room
> for the new data to be stored. However saying anything based on what you
The hard drive has ~120 GB of available free memory.

> have provided would be speculative. Give more information on the error and
> also post the execution part of your script.

>
> Good Luck
> On Sep 9, 2014 2:36 AM, "Viswanath Pasumarthi"
> <v.pasumarthi_at_iitg.ernet.in>
> 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.
>>
>>
>>
>>
>>
>