Hi Thomas,
The first thing that comes to mind is to take the calculated bond distances
obtained from ptraj and plug them directly into the bond portion of the force
field equation (if the atoms are covalently bonded to each other). This can
be done easily using a spreedsheet or a home-made script. The assumption for
this is that the bond energy is due to the localized force (bond stretching
force constant) between those two atoms, and other forces do not contribute
to its value.
Cheers,
Karl
On Wednesday 17 June 2009 16:04, Thomas Lake wrote:
> Hi,
>
> Is there a function for calculating the bond length energy between a
> pair of atoms in a molecule? In my case I want to calculate the bond
> length energy of a disulfide (S-S) bond, as a function of time. I can
> calculate the bond distance using ptraj.
>
> Thanks
>
> Thomas Lake
> Imperial College London
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Received on Mon Jul 06 2009 - 10:06:59 PDT
