Hi Eugene,
Yes Bill is correct. The energies in that table are those for a single structural snapshot and is the bond term in the following two equations:
It is thus merely the sum of kb(b-b0)^2 over all the bonds in the molecule. If all the bonds were at their equilibrium bond length this value would be zero. The differential of this for each bond would be the force due to the bond being stretched or compressed. It is unrelated to the energy needed to break a bond.
All the best
Ross
> On Feb 14, 2017, at 02:02, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> I believe that you are comparing single-point energies (sum of energies
> of bonds in a relaxed molecule of Ala Ala Ala) to the energy it would
> take to rip one instance of the bond apart.
>
> Bill
>
> On 2/13/17 10:47 PM, Eugene Cha wrote:
>> I'm a little confused as to the meaning of the energy term that is produced
>> by sander
>>
>> http://www.rosswalker.co.uk/papers/Int_J_Quant_Chem_2009_109_15_3767-3772_Chamber.pdf
>>
>> For example in this paper in Table 4 the bond energy is expressed as 1.34
>> kcal/mol, but, for example the dissociation bond energy of a single C-C
>> bond is 83 kcal/mol. The paper indicates that the values are the difference
>> between the PSF and COR files. I'm confused as to what that indicates.
>>
>> I've read through the manual and googled as much as I could, but I would
>> really appreciate some help.
>>
>> Thank you
>>
>>
>> Eugene
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 14 2017 - 05:00:02 PST
