-deffnm ignored when using -multidir
I have five directories where I am running five simultaneous free energy simulations. The node I'm running on has 2 GPU's and 20 cores (10 dual core processors). I go into each directory and run gmx grompp as normal. Then I go to the directory just above these and do the following:
mpirun -np 10 gmx mdrun -ntomp 2 -gpu_id 0000011111 -multidir C1 C2 C3 C4 C5 -deffnm min.0
The .tpr file I'm using in each directory (C1 through C5) is named "min.0.tpr", but mdrun gives me an error that "topol.tpr" cannot be found.
Specifying the .tpr file with the "-s" flag makes the error go away:
mpirun -np 10 gmx mdrun -ntomp 2 -gpu_id 0000011111 -multidir C1 C2 C3 C4 C5 -s min.0.tpr -deffnm min.0
But at this point all of the output files still go to the default (e.g., I would expect "min.0.log" to be output in each directory, but instead it is "md.log").
I can run a single simulation in each directory with -deffnm and it works as expected.
It seems that -deffnm is ignored when using -multidir. GROMACS 5.0.5 does not seem to have this issue.