# [gmx-users] Bonds energies calculation

David spoel at xray.bmc.uu.se
Sun May 25 19:28:00 CEST 2003

```On Sun, 2003-05-25 at 14:38, Alexander wrote:
> Hi gromacs developers,
> I have simply topology for Oxygen molecule with bond description:
>  [ bonds ]
> ; atom0   atom1      optimal_length    energy_constant
>     O      O00           0.10860          51730.6
> I have a frame from trajectory(in pdb format):
> MODEL        2
> ATOM      1  O   LIG     1      30.001  29.984  30.000  1.00  0.00
> ATOM      2  O00 LIG     1      29.999  30.016  31.080  1.00  0.00
> TER
> ENDMDL
> I have try to calculate the bond energy in current frame:
> length=sqrt((x[O]-x[O00])^2+(y[O]-y[O00])^2+(z[O]-z[O00])^2)
> length=sqrt(0.000004+0.001024+1.1664)=1.08048 A -> 0.108048nm
> the bond deviation:
> deviation=(length-optimal_length)=0.0005524nm
> and the bond energy is:
> BOND_ENERGY=energy_constant*deviation^2
> BOND_ENERGY=51730.6*(0.0005524)^2=0.0157854 kJ/mol
> but, the same energy extracted by g_energy is:
> energy.xvg
>     0.006000    0.007892
> It seems that round(0.0157854*0.5)=0.007892, but where 0.5 coefficient
> taken from?

it's just a definition of course (see manual), but it is the common
definition of a harmonic potential.

>
> Thank you,
> Best regards,
>
> Alexander Yakovenko
> Institute of Molecular Biology & Genetic of NAS of Ukraine
> 03143
> Kiev
> Ukraine
> ______________________________________________
> E-mail: yakovenko_a at ukr.net
>
>
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--
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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