See Parallel::ForkManager. As in their example:

use Parallel::ForkManager;
my $pm = new Parallel::ForkManager($MAX_PROCESSES);

# ...

foreach my $f (@files) {
  if ( (-d $f) and ($f ne ".") and ($f ne "..") ){
     my $pid = $pm->start and next;
     chdir ...
     system ...
     system ...
     system ...
     $pm->finish;
  }
}
$pm->wait_all_children;
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Update Since ForkManager handles the forking, you will not need to fork/exec mdrun, a system will be fine.

Update Added call to wait_all_children