Hi again.. I guess I figured it out :-) The below seems to work:

sub mdrunner {
    
    my $passed_dir = $_[0];
    my $dirtoget="${passed_dir}/StretchingDecaAlanine/GMXCubicBox/Umbr
+ella";
     my (@directories, @part) = ();
     
     opendir(IMD, $dirtoget) || die("Cannot open directory");
 
     my @files= readdir(IMD);
     closedir(IMD);
     
     foreach my $g (@files) {
         push(@directories, $g) if ((-d $g) and ($g ne ".") and ($g ne
+ ".."));
     }
     
     while(scalar(@directories) > 0) {
        
        #Take first 4 when there are 4 or more elements in the array
        if(scalar(@directories)>=4){
            @part= @directories[0..3];
        }    
        
        #Take as many as possible when <4 elements in the array
        elsif(scalar(@directories)<4){
            @part = @directories [0..scalar(@directories)];

        }
         
         #Shorten the array by the number of elements taken in @part
         for(my $i=0; $i<scalar(@part); $i++) {
            shift(@directories);
        }
        
        #For each element in @part, create children processes
         foreach my $f (@part) {
             
             my $secdirtoget= "${passed_dir}/StretchingDecaAlanine/GMX
+CubicBox/Umbrella/${f}";
             chdir ($secdirtoget);
               
               system ("ln -s ../md_umbrella.mdp ../index.ndx ../topol
+.top ../posre_CTerm.itp ../posre.itp .");
               system ("grompp -f md_umbrella.mdp -c pullconf.gro -n i
+ndex.ndx");
               
               my $pid = fork();
               
               if ($pid == -1) {
                   die;
               } 
               
               elsif ($pid == 0) {
                   print "Running mdrun for within $f\n";
                   exec 'mdrun', '>logje 2>&1 &' or die;
              }
            
            chdir ("${passed_dir}/StretchingDecaAlanine/GMXCubicBox/Um
+brella");
         }
        while (wait() != -1) {}
        print "Done with mdrun in"."@part\n";
     }
}
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