From: Jan Saam (saam_at_charite.de)
Date: Mon Aug 27 2007 - 03:47:04 CDT
Dear Venky,
The energy minimum is the most important region because this region will
be accessed more often during the MD simulation than the barriers. You
should try to fit the dihedral function around the minimum at -180/180
deg. Unless you are particularly interested in the barrier crossing this
should be fine. In case you want to properly describe the barrier
region, too, you can use the dihedral expansion, i.e. you define a
dihedral with multiplicity>1 where you have several terms with different
periodicities for one dihedral.
Jan
Venky schrieb:
> Hi,
>
>
> I am trying to parameterize a small molecule using ab-initio
> calculations and I am new to parameterization. I have a few questions
> regarding Dihedral angle parameter determination.
> I optimized the geometry of my molecule and used the lowest energy
> configuration to generate Potential energy surface scan of a
> particular dihedral angle rotation (rigid PES scan without
> optimization at each rotation) and below are the energies obtained
> from the calculation.
>
>
> *******************************************
> Summary of the potential surface scan:
>
>
> N t16(deg) SCF
> ---- --------- -----------
> 1 -179.9018 -1782.33483
> 2 -167.9018 -1782.33287
> 3 -155.9018 -1782.32715
> 4 -143.9018 -1782.31720
> 5 - 131.9018 -1782.30308
> 6 -119.9018 -1782.28451
> 7 -107.9018 -1782.26171
> 8 -95.9018 -1782.23616
> 9 -83.9018 -1782.21000
> 10 -71.9018 -1782.18683
> 11 -59.9018 -1782.16332
> 12 -47.9018 -1782.11096
> 13 -35.9018 -1781.95668
> 14 -23.9018 -1781.55212
> 15 -11.9018 -1780.77154
> 16 0.0982 -1780.21021
> 17 12.0982 -1780.77625
> 18 24.0982 -1781.55508
> 19 36.0982 -1781.95792
> 20 48.0982 -1782.11159
> 21 60.0982 -1782.16350
> 22 72.0982 -1782.18703
> 23 84.0982 -1782.21022
> 24 96.0982 -1782.23629
> 25 108.0982 -1782.26192
> 26 120.0982 -1782.28451
> 27 132.0982 -1782.30301
> 28 144.0982 -1782.31721
> 29 156.0982 -1782.32717
> 30 168.0982 -1782.33291
> 31 180.0982 -1782.33483
> ---- --------- -----------
>
> The graph is a single spike at 0 degrees with two minima at 180 and
> -180. I tried to fit the data using the dihedral parameter equation...
> V=Kchi(1+cos((n*chi)-d)) but the plot doesn't look like a cosine
> curve. rather the energy rise is steep at its maximum (near 0 degrees)
> and the data doesn't fit the equation.
> I used n=1, d=0 and varied Kchi over chi= -180 to 180.
>
> Is the procedure followed by me the right way to go about dihedral
> parameterization? If then how do I go about fitting the PES energies
> to the Dihedral equation.
>
>
> Thanks a lot in advance...
>
> Venky
-- --------------------------- Jan Saam Institute of Biochemistry Charite Berlin Monbijoustr. 2 10117 Berlin Germany +49 30 450-528-446 saam_at_charite.de
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