I would like to estimate the free energy over different time ranges of the production trajectory in an FEP simulation. Can I do that?

Yes. To do so you will need to use the bennett.py script. To get a usage statement, enter:

$SCHRODINGER/run -FROM desmond bennett.py -h

To run the bennett.py script manually, you will need to locate, collect, and rename a few files. First, you will need to find the .dE files from the production run trajectory, which should be stage 11. That is, you need to unpack the following .tgz file:

jobname_11-out.tgz

Inside, you will need to locate the .dE files, which are named according to this scheme:

jobname_11_lambdalambda#.lambda#.dE

Copy all of these files into a new directory, and rename the files according to this scheme:

gibbs.lambda#.dE

You can then run bennett.py using a command along the lines of:

$SCHRODINGER/run -FROM desmond bennett.py -b 150.0 -e 600.0 -F 2 -R 1 -T 298.15 -s gibbs.%d.dE -l 0 -L 11 -o 150_600.result

This will instruct bennett.py to estimate the dG values for the time range from 150 to 600 ps.

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