Hi gmx-users,
Can anyone tell me how to find the total energy of the protein only (not the
system)?
You might try energygrp_excl SOL SOL
or energygrp_excl SOL SOL SOL PROTEIN
depending on what you want to acheive. THis will take care of all of
the nonbonded interactions.
Without knowing what you want this value for, I can only warn you
against trying to use this value as a measure of how "good" the
structure is.
What I've done is I minimized the system first, then I took out the water
from the pdb file, then minimized it again without water, and get the total
energy from the log file.
Why do a solvated minimization when you are then going to do a
minimization in vaccuum?
But when I'm comparing the result to get the delta Emm, the result did not
make any sense.
Did not make sense how? We can't help without knowing what the problem is.
Can someone help me on this please.
Thank you very much,
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