Thank you both for the clarification. Especially with regards to the
negative terms implying a further expansion of the fourier series.
On Mon, Feb 15, 2010 at 12:42 PM, Jason Swails <jason.swails.gmail.com> wrote:
> This is true.
>
> On Mon, Feb 15, 2010 at 11:07 AM, Ilyas Yildirim
> <yildirim.pas.rochester.edu> wrote:
>> What exactly do you mean with 'the function is only fit to a single fourier
>> term' ? The E_tors can have as many cosine terms in it as possible. For
>> instance, in the parm99.dat file, you have the following torsion defined:
>>
>> CT-CT-CT-CT 1 0.18 0.0 -3.
>
> The negative in the last column means include another term. The
> positive value is actually used for the parameter. Once a
> non-negative value is set for the last column, no further fourier
> terms are used for that torsion (and I'm guessing that if the values
> were positive, each successive term would overwrite the last if it
> didn't throw an error message).
>
>> CT-CT-CT-CT 1 0.25 180.0 -2.
>> CT-CT-CT-CT 1 0.20 180.0 1.
>>
>> This parameter set is to define the torsion energy of CT-CT-CT-CT with
>> different PHASE, PK, and PN values (IDIVF is equal to 1) which will have 3
>> cosine term to define the CT-CT-CT-CT torsional energy. You can increase the
>> level of accuracy by increasing the number of cosine terms used to define a
>> particular torsion.
>>
>> Ilyas Yildirim, Ph.D.
>> ---------------------------------------------------------------
>> = Hutchison Hall B#10 - Department of Chemistry =
>> = - University of Rochester =
>> = 585-275-6766 (office) - =
>> = http://www.pas.rochester.edu/~yildirim/ =
>> ---------------------------------------------------------------
>>
>> On Mon, 15 Feb 2010, stephane acoca wrote:
>>
>>> Hi, I would like to clarify the protocol for adjusting torsional
>>> parameters. The problem I am having is that after fitting to a fourier
>>> series the energy difference between the QM and MM energies (torsion
>>> not included in MM Energy), the frcmod specifications I find point to
>>> :
>>>
>>> IDIVF
>>> PK
>>> PHASE
>>> PN
>>>
>>> Meaning that the function is only fit to a single fourier term of the
>>> format :
>>>
>>> Etors = (PK/IDIVF)*(1+ COS(PN*PHI - PHASE)
>>>
>>> Aren't higher level fourier terms available to be specified torsion
>>> parameters. I couldn't find the information in either Amber manual
>>> 8,9, or 10. Any guidance would be appreciated.
>>>
>>> Stephane Acoca
>>> McGill University
>
>
> Good luck!
> Jason
>
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
>
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Received on Mon Feb 15 2010 - 14:00:02 PST
