#!/usr/bin/env perl use strict; use warnings; use File::Path qw/make_path/; use Cwd; my $dir = cwd(); opendir (DIR, $dir) or die "Unable to open current directory! $!\n"; my @subdirs = readdir (DIR) or die "Unable to read directory! $!\n"; closedir DIR; my $result_path = "$dir/results"; make_path("$result_path"); foreach my $subdir ( sort @subdirs ) { chdir($subdir) or die "Cannot cd to $dir: $!\n"; make_path("$result_path/$subdir"); system("echo '1 0' | program -f methane.trr -o $result_path/$subdir/outfile.txt"); chdir(".."); }