[gmx-users] Ask about improper angle energy

[Anton Feenstra]

alexander yakovenko wrote:
> Dear gromacs developers, 
>  
> I have the structure of formaldehyde molecule: 
[...]
> and energy of improper angle from energy.xvg: 
>     0.001000    0.043663 
>  
>   But the calculated improper is: 
>   1.328Deg->0.0232Rad 
>   The formula of improper energy from GROMACS manual is: 
>   E=k*(value-optimal_value)^2 
>  
>   and E=564.36*(0.0232)^2=0.3029 
> that is  substantialy higher than extracted from trajectory. 
> Would you please to help me to find mistake in my calculations? 

Using rasmol2.7, I measured the improper dihedral angle to be
0.6 degrees, which is different from your 1.3. How did you
obtain/calculate your angle?


-- 
Groetjes,

Anton
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|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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