Hi Adrian,
Thank you for filling in for my obvious lack of my experience in this
area. I think that may have completely resolved the issue I am having.
Many thanks again
Anthony
On 15/10/2015 19:53, "Adrian Roitberg" <roitberg.ufl.edu> wrote:
>Hi Anthony
>
>When people write 'hessian', they really mean mass weighted hessian.
>That is the object you diagonalize to get normal modes, which you then
>project onto bonds.
>
>That mass weighting is what makes the force on an H and on a C the SAME
>for H-C
>
>is that ok ?
>
>adrian
>
>
>On 10/15/15 2:47 PM, Nash, Anthony wrote:
>> Hi Dac,
>>
>> Many thanks for your input, I appreciate it.
>>
>> Completely agree with you, which is why I am extremely confused how a
>> number (and not a small one) of publications have claimed to use second
>> order derivation of cartesian coordinates (hessian) from QM
>>calculations.
>> An extensive example: "Systematic Derivation of AMBER Force Field
>> Parameters
>> Applicable to Zinc-Containing Systems². In their abstract:
>>
>> ³...In this study, we have derived bond stretching and angle-bending
>> parameters applicable to zinc-containing systems which are compatible
>>with
>> the AMBER force field. A total of 18 model systems were used to mimic
>>the
>> common coordination configurations observed in the complexes formed by
>> zinc-containing metalloproteins. The Hessian matrix of each model system
>> computed at the B3LYP/6-311++G(2d,2p) level was then analyzed by
>> Seminario¹s method to derive the desired force Constants.."
>>
>> Many thanks
>> Anthony
>>
>>
>>
>> On 15/10/2015 17:35, "David A Case" <dacase.scarletmail.rutgers.edu>
>>wrote:
>>
>>> On Thu, Oct 15, 2015, Nash, Anthony wrote:
>>>> the force constant for A-B is not the same as B-A.
>>>> So using second
>>>> order tensors, the force constant for C-H is much greater than the
>>>> force constant for H-C (where C is seen is the displacing atom, and H
>>>> experiences the force).
>>>>
>>> This is not the way molecular mechanics potentials work. The bond
>>>energy
>>> doesn't know anything about what is the "displacing atom". It just
>>>looks
>>> at the distance from one atom to the next (which clearly doesn't depend
>>> upon
>>> which order is used.)
>>>
>>> If you wish to fit molecular mechanics potentials to quantum data,
>>>there
>>> are
>>> lots of tools that will help do that. But I don't know of any that
>>>start
>>> from
>>> the sort of non-symmetric tensors that you are thinking of.
>>>
>>> Maybe someone on the list will be able to chime in.
>>>
>>> ....dac
>>>
>>>
>>> _______________________________________________
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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>
>--
>Dr. Adrian E. Roitberg
>Professor.
>Department of Chemistry
>University of Florida
>roitberg.ufl.edu
>352-392-6972
>
>
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Received on Thu Oct 15 2015 - 12:00:07 PDT
