[gmx-users] Why are the bond and angle energy at the first step of energy minimization not equal 0?

[Hoa Trinh]

Hi Gromacs user,
I am following a Gromacs tutorial on the website of Dr. Justin:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.html

After performing energy minimization, I open the log file and see that at
time step = 0 (time = 0.000), bond energy and angle energy are not equal 0.
Given that: E_bond = 0.5*k*(r-r0)^2
At t = 0: r = r0, therefore E_bond should be approximate 0.
Please correct me.
Thank you.
Best regards,
*Lan Hoa*