[gmx-users] BOND ... ANGLE and TORSION energy discrepancy between gromacs and cp2k

[Justin Lemkul]

On 8/9/13 10:33 AM, Golshan Hejazi wrote:
> Hello,
>
> Thanks for the reply. I made another even more simple test. I just would like to understand what is going on inside the energy calculation. I have an ALA system. This is the topology file for the bond:
>
> [ bonds ]
> ;  ai    aj funct  r  k
>      1     2     1  1.0100e-01  3.6317e+05
>      3     4     1  1.0900e-01  2.8451e+05
>      5     6     1  1.0900e-01  2.8451e+05
>      5     7     1  1.0900e-01  2.8451e+05
>      5     8     1  1.0900e-01  2.8451e+05
>      1     3     1  1.4490e-01  2.8200e+05
>      3     5     1  1.5260e-01  2.5941e+05
>      3     9     1  1.5220e-01  2.6527e+05
>      9    10     1  1.2290e-01  4.7698e+05
>
>  From here, I computed manually the bond energy which is : sum (ki*(r_i*r_i)) = 42536.87 (kj/mol)
> however, when I perform a rerun on the gro file ... this is the bond energy: 2.20074e-01 (kj/mol)
>
> What am I missing?

It looks like you're calculating the bonded energy wrong.  The energy is 
calculated from the distance the bond length is from the equilibrium value, not 
the bond length itself.  See the manual for the necessary equation.

-Justin

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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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