[gmx-users] How to include bonded parameters in ffgmxbon.itp?

[Erik Lindahl]

K.A. Feenstra wrote:

>Alexandre Suman de Araujo wrote:
>
>>But my problem is not the bond lenght, this value I have. But the problem is
>>the K parameter... where can I find or calculate it for each type of atom?!
>>Thank's!
>>
>
>You might not need them, if you want to *constrain* bond lengths (using
>either Shake or Lincs). Otherwise, I think they are usually derived
>from IR spectrometry frequencies... But, you could simply take values
>from appropriate existing bond types, they won't be too critical.
>
They won't matter at all once you use the constraints, but since you 
might want to use flexible
bonds e.g. with conjugate gradients minimization it's a good idea to 
have bond constants in the
right order of magnitude at least...

Cheers,

Erik