sub mdrunner {
	
	my $passed_dir = $_[0];
	my $dirtoget="${passed_dir}/StretchingDecaAlanine/GMXCubicBox/Umbrella";
 	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/GMXCubicBox/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 index.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/Umbrella");
 		}
		while (wait() != -1) {}
		print "Done with mdrun in"."@part\n";
 	}
}