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 - 10:00:03 PST
