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

Peter Zoon zoon at science.uva.nl
Sat Mar 27 09:29:01 CET 2004

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.


At 09:18 3/27/2004, you wrote:
>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.
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>gmx-users at gromacs.org
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