you are right about the pmemd. However it has multiple output files.

But you only wish to monitor one of them, right?

If so, then do as I suggested above, but with the extra options required. And if you need to retain the file (mdout) that would have been produced had you not redirected it, just write it yourself as you monitor the output.

On Win*, it might look something like:

my $pid = open KID,  '-|', 
    'pmemd -i mdin -c inpcrd -p prmtop -r restrt -o con -x mdcrd' 
    or die $!;

open OUT, '>', 'mdout' or die $!;

while( <KID> ) {
    kill 'INT', $pid if m[some data];
    print OUT;
}
[download]

Again, I don't know the correct syntax for *nix. Maybe something like this would work?:

my $pid = open KID,  '-|', 
    qq[pmemd -i mdin -c inpcrd -p prmtop -r restrt -o /dev/tty -x mdcr
+d] 
    or die $!;

open OUT, '>', 'mdout' or die $!;

while( <KID> ) {
    kill 'INT', $pid if m[some data];
    print OUT;
}
[download]

Note the use of the list form of open to avoid a shell process.