Positive energy values for protein

From: Ashkan Shekaari (shekaari_at_email.kntu.ac.ir)
Date: Sat Dec 01 2018 - 07:43:48 CST

Dear Experts,

When I try to extract the total energy of my protein solvated in a water sphere using NAMDEnergy of VMD,
the values in each timestep are positive. Moreover, the total energies associated with the whole system as well as
the water sphere itself are both negative (E_tot < E_water_sphere).
1- Is anything wrong with my calculations?
2- Is the difference ( E_tot - E_water_sphere) equal to the energy value of the protein itself?
If so, where does such a contradicting difference come from?

Ashkan Shekaari, 
Ph.D Candidate in Solid State Physics, 
K. N. Toosi University of Technology, 
Tehran, Iran 
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