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

Justin Lemkul jalemkul at vt.edu
Sat Mar 17 19:02:40 CET 2018

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 A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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