I have a few other questions. I understand that the PK values correspond to
the coefficients that were obtained during the fitting of the Fourier
series. The coefficients are divided by 2 and the resulting value is the PK
value. The form of the series that I used did not contain a PHASE parameter
(it was set to 0).I am assuming that this infers that the PHASE value must
be set to 0 for the torsion parameter but wanted to clarify the matter.
Form used : *PK**1/2 (1+COS(*PN**phi - 0))
Stephane Acoca
McGill University
On Mon, Feb 15, 2010 at 4:49 PM, stephane acoca <stephane.acoca.gmail.com>
wrote:
> 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
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Wed Feb 17 2010 - 08:30:02 PST
