#!/usr/bin/perl
use strict;
use warnings;

my @steps = ( 'ele1.0', 'ele0.5' );

die if @steps < 2; 
open my $MIN_RUN, '>', 'run'
    or die "Cannot open 'run': $!";

my $last_step = $steps[0];
for my $step ( @steps[1..$#steps] ) {
    print $MIN_RUN "/opt/sander -i $step.min -p ../$step.prmtop -o $step$step.e &\n";
    print $MIN_RUN "/opt/sander -i $step.min -p ../../$last_step/$last_step.prmtop -o $step$last_step.e &\n";
    $last_step = $step;
}

close $MIN_RUN or warn;