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

[Justin Lemkul]

On 3/17/18 1:56 PM, Hoa Trinh wrote:
> 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.

Simply, r =/= r0 at t = 0 (and in energy minimization it's not time, 
it's step number).

Unless a structure was built *exactly* according to the force field 
parameters in terms of equilibrium bond lengths and valence angles, you 
will never have a zero value for these terms. Experimental structures 
certainly never conform exactly to these parameters, nor will they 
throughout the simulation.

-Justin

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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

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