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

Erik Lindahl lindahl at stanford.edu
Thu Sep 26 09:41:58 CEST 2002

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?!
>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...



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