bug(?) with -multidir and single directory
'mdrun -multidir my_directory' behaves the same as simply 'mdrun', i.e. starts to look for a tpr in the current directory. A better behavior in my opinion would be to either 1) start running in "my_directory" or 2) give an error.
Handle multidir/multisim with single argument correctly
Mdrun would only initialize the multi option correctly
with more than one argument, which caused mdrun to fail
in strange ways since it looked for topol.tpr in the
current directory instead.