[gmx-users] Extending an mdrun with trr >2GB

[Martina Bertsch, PhD]

If I understand correctly, trjconv converts the trr file to xtc format, 
which does *not* contain velocities or forces and thus saves space. 
Manuals specifically instruct us not to remove the trr file if a run has 
to be restarted.

I don't think I would get a true continuation run without velocities. Am 
I correct?

Martina 

Peter Zoon wrote:

> Hi!
> with trjconv you can make full.trr smaller and thus overcome the 
> problem of file> 2GB
> Then you can use this newly made file to restart, with tpbconv.
>
> Cheers
> Peter
>
> At 09:18 3/27/2004, you wrote:
>
>> Greetings.
>>
>> Our administrator had to install upgrades on the cluster, so I had to 
>> stop my mdrun of a protein in a POPC bilayer, which was running 
>> smoothly up until now (for 10 ns). To stop the run, I used the kill 
>> -USR1 signal. The signal produced a gro file, named 
>> "MT1_popc_postfull.gro", and the megaflops accounting report at the 
>> end of the log file, as if it were the end of the run. However, the 
>> run would have been continued for another 10 ns, if there had not 
>> been any interruption.
>>
>> When the upgrades were completed, I attempted to restart the run with 
>> the following command:
>>
>> tpbconv -s full.tpr -f full.trr -o full_extend_1.tpr -extend 10000
>>
>> I also tried the following:
>>
>> grompp -f full.mdp -t full.trr -c MT1_popc_postfull.gro -n index.ndx 
>> -p MT1_popc.top -o full_extend.tpr
>>
>> But in both cases, I received an error message:
>>
>> File full.trr not found.
>>
>> Of course, the file is actually present and larger than 2.2 GB.
>>
>> How do I continue/extend my mdrun? I could start a new 10 ns 
>> simulation with the final coordinates from MT1_popc_postfull.gro, but 
>> it would not be a true continuation run without the velocities from 
>> the first part of the run, since I could not read the trr file.
>>
>> Also, will I be able to analyze the trr trajectory that is larger 
>> than 2 GB with g_rms, g_hbond etc, or will I have to convert it to 
>> the xtc format?
>>
>> Thank you.
>>
>> Martina
>>
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