[gmx-users] stress-strain using pull code

[Ali Khodayari]

Dear all,
I am trying to compute the stress-strain curves, using the pull code explained in Justin’s tutorial. I want to put my crystalline cellulose (which is solvated in water) under tension force at room temperature, and compute the nano-mechanical properties of the system, e.g. Yield modulus, etc.
How can I relate the potential (energies) of the output edr file to this end? In other words, are the output energies, after tension, absolute values or they are relative values to the time when there have been no tension applied yet?
How can I obtain the energy values of only a group of my system out of the edr file? Since I assume the output is, by default, the total averaged energies of the system, while I have no interest in contribution of the part coming from water.
Best,
Ali