Yes, you are right about the pmemd. However it has multiple output files. The whole command looks something like this:

pmemd -i mdin -c inpcrd -p prmtop -r restrt -o mdout -x mdcrd

restrt mdout and mdcrd are outputs while mdout is the one I am going to moniter changes.
So how do you specify that very file in open?

In reply to Re^2: How to monitor a child process from a perl script by oscarjiao
in thread How to monitor a child process from a perl script by oscarjiao

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