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

[Martina Bertsch, PhD]

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