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

[Hoa Trinh]

Great explanation! Thank you very much.

*Lan Hoa*

2018-03-17 13:02 GMT-05:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> 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.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
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