my $passed_dir = $_[0];
	my $dirtoget="${passed_dir}/StretchingDecaAlanine/GMXCubicBox/Umbrella";
 	
 	opendir(IMD, $dirtoget) || die("Cannot open directory");
 
 	my @files= readdir(IMD);
 	closedir(IMD);
 	
 	foreach my $f (@files) {
 		
		if ( (-d $f) and ($f ne ".") and ($f ne "..") ){
 
 			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;
 			 }
       		
       		while (wait() != -1) {}
			
                        print "Done with mdrun in $f\n";
			
			chdir ("${passed_dir}/StretchingDecaAlanine/GMXCubicBox/Umbrella");
		}